; 2012-07-02.203256 peak-motifs -v 1 -title p300_heart_versus_limb_Blow2010 -i $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/peak-motifspeak_seq -ctrl $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/peak-motifscontrol_seq -markov auto -disco oligos -nmotifs 5 -minol 6 -maxol 7 -2str -motif_db jaspar_core_vertebrates tf $RSAT/public_html/data/motif_databases/JASPAR/jaspar_core_vertebrates_2009_10.tf -motif_db jaspar_pbm_mouse tf $RSAT/public_html/data/motif_databases/JASPAR/jaspar_pbm_mouse_2009_10.tf -motif_db custom_motif_collection tf $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/peak-motifs_custom_motif_db.tf -source galaxy -task purge,seqlen,composition,disco,merge_words,collect_motifs,motifs_vs_motifs,timelog,archive,synthesis,motifs_vs_db,motifs_vs_db,scan -prefix peak-motifs -noov -img_format png -outdir $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg ; 2012-07-02.203256 rsync -ruptl $RSAT/perl-scripts/lib/images/arrow*.gif $RSAT/perl-scripts/lib/images/UCSC_icon.jpg $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/images_html ; 2012-07-02.203256 $RSAT/perl-scripts/convert-seq -i $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/peak-motifspeak_seq -from fasta -to fasta -mask non-dna -o $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/data/sequences/peak-motifs_test.fasta ; 2012-07-02.203256 $RSAT/perl-scripts/purge-sequence -dna -i $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/data/sequences/peak-motifs_test.fasta -ml 30 -mis 0 -o $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/data/sequences/peak-motifs_test_purged_ml30_mis0.fasta ; 2012-07-02.203257 $RSAT/perl-scripts/sequence-lengths -i $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/data/sequences/peak-motifs_test_purged_ml30_mis0.fasta -o $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/data/sequences/peak-motifs_test_seqlen.tab ; $RSAT/perl-scripts/classfreq -v 1 -col 2 -i $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/data/sequences/peak-motifs_test_seqlen.tab -ci 20 -o $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/data/sequences/peak-motifs_test_seqlen_distrib.tab ; 2012-07-02.203257 $RSAT/perl-scripts/XYgraph -lines -pointsize 0 -legend -format png -title 'Sequence lengths; p300_heart_versus_limb_Blow2010' -ysize 200 -ycol 4 -yleg1 'Number of peaks' -xsize 800 -xcol 3 -xleg1 'Peak length' -xmin 0 -ymin 0 -i $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/data/sequences/peak-motifs_test_seqlen_distrib.tab -o $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/data/sequences/peak-motifs_test_seqlen_distrib.png ; 2012-07-02.203258 $RSAT/perl-scripts/convert-features -i $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/peak-motifspeak_seq -from galaxy_seq -to bed | sed '1s/^.*/track name="test_peaks" description="RSAT peak-motifs p300_heart_versus_limb_Blow2010 test: peaks" visibility=2 use_score=1 color=13,115,67/' > $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/data/sequences/peak-motifs_test_seqcoord.bed ; 2012-07-02.203258 time ($RSAT/bin/count-words -v 1 -i $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/data/sequences/peak-motifs_test_purged_ml30_mis0.fasta -l 1 -1str > $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/composition/peak-motifs_test_freq-1str-ovlp_1nt.tab) >& $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/composition/peak-motifs_test_freq-1str-ovlp_1nt.tab_time.txt ; 2012-07-02.203258 $RSAT/perl-scripts/convert-background-model -from oligos -to inclusive -i $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/composition/peak-motifs_test_freq-1str-ovlp_1nt.tab -o $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/composition/peak-motifs_test_inclusive-1str-ovlp_1nt.txt; $RSAT/perl-scripts/convert-background-model -from oligos -to transitions -i $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/composition/peak-motifs_test_freq-1str-ovlp_1nt.tab -o $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/composition/peak-motifs_test_transitions-1str-ovlp_1nt.tab ; cut -f 1-5,7 $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/composition/peak-motifs_test_transitions-1str-ovlp_1nt.tab | $RSAT/perl-scripts/draw-heatmap -min 0 -max 1 -out_format png -col_width 50 -o $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/composition/peak-motifs_test_heatmap-1str-ovlp_1nt.png ; 2012-07-02.203258 time ($RSAT/bin/count-words -v 1 -i $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/data/sequences/peak-motifs_test_purged_ml30_mis0.fasta -l 2 -1str > $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/composition/peak-motifs_test_freq-1str-ovlp_2nt.tab) >& $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/composition/peak-motifs_test_freq-1str-ovlp_2nt.tab_time.txt ; 2012-07-02.203258 $RSAT/perl-scripts/convert-background-model -from oligos -to inclusive -i $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/composition/peak-motifs_test_freq-1str-ovlp_2nt.tab -o $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt; $RSAT/perl-scripts/convert-background-model -from oligos -to transitions -i $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/composition/peak-motifs_test_freq-1str-ovlp_2nt.tab -o $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/composition/peak-motifs_test_transitions-1str-ovlp_2nt.tab ; cut -f 1-5,7 $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/composition/peak-motifs_test_transitions-1str-ovlp_2nt.tab | $RSAT/perl-scripts/draw-heatmap -min 0 -max 1 -out_format png -col_width 50 -o $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/composition/peak-motifs_test_heatmap-1str-ovlp_2nt.png ; 2012-07-02.203259 time ($RSAT/perl-scripts/position-analysis -v 1 -i $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/data/sequences/peak-motifs_test_purged_ml30_mis0.fasta -format fasta -sort -return chi,sig,distrib,graphs,rank -max_graphs 20 -1str -ovlp -seqtype dna -l 1 -ci 20 -img_format png -title 'p300_heart_versus_limb_Blow2010' -origin center -o $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/composition/peak-motifs_test_profiles-1str-ovlp_1nt_ci20.tab) >& $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/composition/peak-motifs_test_profiles-1str-ovlp_1nt_ci20.tab_time.txt ; 2012-07-02.203309 grep -v ";" $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/composition/peak-motifs_test_profiles-1str-ovlp_1nt_ci20.tab | cut -f 1,10-10000 | $RSAT/perl-scripts/transpose-table | $RSAT/perl-scripts/XYgraph -xcol 1 -ycol 2-5 -format png -legend -lines -pointsize 0 -legend -header -colors $RSAT/perl-scripts/lib/color_palettes/1nt-1str_colors.tab -title 'Nucleotide composition profiles : ; test sequence; p300_heart_versus_limb_Blow2010' -xleg1 'Position' -xsize 800 -yleg1 'Occurrences' -ysize 300 -ymin 0 -o $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/composition/peak-motifs_test_profiles-1str-ovlp_1nt_ci20.png ; 2012-07-02.203309 time ($RSAT/perl-scripts/position-analysis -v 1 -i $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/data/sequences/peak-motifs_test_purged_ml30_mis0.fasta -format fasta -sort -return chi,sig,distrib,graphs,rank -max_graphs 20 -1str -ovlp -seqtype dna -l 2 -ci 20 -img_format png -title 'p300_heart_versus_limb_Blow2010' -origin center -o $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/composition/peak-motifs_test_profiles-1str-ovlp_2nt_ci20.tab) >& $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/composition/peak-motifs_test_profiles-1str-ovlp_2nt_ci20.tab_time.txt ; 2012-07-02.203323 grep -v ";" $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/composition/peak-motifs_test_profiles-1str-ovlp_2nt_ci20.tab | cut -f 1,10-10000 | $RSAT/perl-scripts/transpose-table | $RSAT/perl-scripts/XYgraph -xcol 1 -ycol 2-17 -format png -legend -lines -pointsize 0 -legend -header -colors $RSAT/perl-scripts/lib/color_palettes/2nt-1str_colors.tab -title 'Dinucleotide composition profiles : ; test sequence; p300_heart_versus_limb_Blow2010' -xleg1 'Position' -xsize 800 -yleg1 'Occurrences' -ysize 300 -ymin 0 -o $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/composition/peak-motifs_test_profiles-1str-ovlp_2nt_ci20.png ; 2012-07-02.203324 $RSAT/perl-scripts/convert-seq -i $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/peak-motifscontrol_seq -from fasta -to fasta -mask non-dna -o $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/data/sequences/peak-motifs_ctrl.fasta ; 2012-07-02.203324 $RSAT/perl-scripts/purge-sequence -dna -i $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/data/sequences/peak-motifs_ctrl.fasta -ml 30 -mis 0 -o $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/data/sequences/peak-motifs_ctrl_purged_ml30_mis0.fasta ; 2012-07-02.203324 $RSAT/perl-scripts/sequence-lengths -i $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/data/sequences/peak-motifs_ctrl_purged_ml30_mis0.fasta -o $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/data/sequences/peak-motifs_ctrl_seqlen.tab ; $RSAT/perl-scripts/classfreq -v 1 -col 2 -i $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/data/sequences/peak-motifs_ctrl_seqlen.tab -ci 20 -o $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/data/sequences/peak-motifs_ctrl_seqlen_distrib.tab ; 2012-07-02.203325 $RSAT/perl-scripts/XYgraph -lines -pointsize 0 -legend -format png -title 'Sequence lengths; p300_heart_versus_limb_Blow2010' -ysize 200 -ycol 4 -yleg1 'Number of peaks' -xsize 800 -xcol 3 -xleg1 'Peak length' -xmin 0 -ymin 0 -i $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/data/sequences/peak-motifs_ctrl_seqlen_distrib.tab -o $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/data/sequences/peak-motifs_ctrl_seqlen_distrib.png ; 2012-07-02.203325 time ($RSAT/bin/count-words -v 1 -i $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/data/sequences/peak-motifs_ctrl_purged_ml30_mis0.fasta -l 1 -1str > $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/composition/peak-motifs_ctrl_freq-1str-ovlp_1nt.tab) >& $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/composition/peak-motifs_ctrl_freq-1str-ovlp_1nt.tab_time.txt ; 2012-07-02.203325 $RSAT/perl-scripts/convert-background-model -from oligos -to inclusive -i $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/composition/peak-motifs_ctrl_freq-1str-ovlp_1nt.tab -o $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/composition/peak-motifs_ctrl_inclusive-1str-ovlp_1nt.txt; $RSAT/perl-scripts/convert-background-model -from oligos -to transitions -i $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/composition/peak-motifs_ctrl_freq-1str-ovlp_1nt.tab -o $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/composition/peak-motifs_ctrl_transitions-1str-ovlp_1nt.tab ; cut -f 1-5,7 $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/composition/peak-motifs_ctrl_transitions-1str-ovlp_1nt.tab | $RSAT/perl-scripts/draw-heatmap -min 0 -max 1 -out_format png -col_width 50 -o $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/composition/peak-motifs_ctrl_heatmap-1str-ovlp_1nt.png ; 2012-07-02.203325 time ($RSAT/bin/count-words -v 1 -i $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/data/sequences/peak-motifs_ctrl_purged_ml30_mis0.fasta -l 2 -1str > $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/composition/peak-motifs_ctrl_freq-1str-ovlp_2nt.tab) >& $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/composition/peak-motifs_ctrl_freq-1str-ovlp_2nt.tab_time.txt ; 2012-07-02.203325 $RSAT/perl-scripts/convert-background-model -from oligos -to inclusive -i $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/composition/peak-motifs_ctrl_freq-1str-ovlp_2nt.tab -o $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/composition/peak-motifs_ctrl_inclusive-1str-ovlp_2nt.txt; $RSAT/perl-scripts/convert-background-model -from oligos -to transitions -i $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/composition/peak-motifs_ctrl_freq-1str-ovlp_2nt.tab -o $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/composition/peak-motifs_ctrl_transitions-1str-ovlp_2nt.tab ; cut -f 1-5,7 $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/composition/peak-motifs_ctrl_transitions-1str-ovlp_2nt.tab | $RSAT/perl-scripts/draw-heatmap -min 0 -max 1 -out_format png -col_width 50 -o $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/composition/peak-motifs_ctrl_heatmap-1str-ovlp_2nt.png ; 2012-07-02.203326 time ($RSAT/perl-scripts/position-analysis -v 1 -i $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/data/sequences/peak-motifs_ctrl_purged_ml30_mis0.fasta -format fasta -sort -return chi,sig,distrib,graphs,rank -max_graphs 20 -1str -ovlp -seqtype dna -l 1 -ci 20 -img_format png -title 'p300_heart_versus_limb_Blow2010' -origin center -o $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/composition/peak-motifs_ctrl_profiles-1str-ovlp_1nt_ci20.tab) >& $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/composition/peak-motifs_ctrl_profiles-1str-ovlp_1nt_ci20.tab_time.txt ; 2012-07-02.203335 grep -v ";" $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/composition/peak-motifs_ctrl_profiles-1str-ovlp_1nt_ci20.tab | cut -f 1,10-10000 | $RSAT/perl-scripts/transpose-table | $RSAT/perl-scripts/XYgraph -xcol 1 -ycol 2-5 -format png -legend -lines -pointsize 0 -legend -header -colors $RSAT/perl-scripts/lib/color_palettes/1nt-1str_colors.tab -title 'Nucleotide composition profiles : ; ctrl sequence; p300_heart_versus_limb_Blow2010' -xleg1 'Position' -xsize 800 -yleg1 'Occurrences' -ysize 300 -ymin 0 -o $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/composition/peak-motifs_ctrl_profiles-1str-ovlp_1nt_ci20.png ; 2012-07-02.203335 time ($RSAT/perl-scripts/position-analysis -v 1 -i $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/data/sequences/peak-motifs_ctrl_purged_ml30_mis0.fasta -format fasta -sort -return chi,sig,distrib,graphs,rank -max_graphs 20 -1str -ovlp -seqtype dna -l 2 -ci 20 -img_format png -title 'p300_heart_versus_limb_Blow2010' -origin center -o $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/composition/peak-motifs_ctrl_profiles-1str-ovlp_2nt_ci20.tab) >& $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/composition/peak-motifs_ctrl_profiles-1str-ovlp_2nt_ci20.tab_time.txt ; 2012-07-02.203348 grep -v ";" $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/composition/peak-motifs_ctrl_profiles-1str-ovlp_2nt_ci20.tab | cut -f 1,10-10000 | $RSAT/perl-scripts/transpose-table | $RSAT/perl-scripts/XYgraph -xcol 1 -ycol 2-17 -format png -legend -lines -pointsize 0 -legend -header -colors $RSAT/perl-scripts/lib/color_palettes/2nt-1str_colors.tab -title 'Dinucleotide composition profiles : ; ctrl sequence; p300_heart_versus_limb_Blow2010' -xleg1 'Position' -xsize 800 -yleg1 'Occurrences' -ysize 300 -ymin 0 -o $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/composition/peak-motifs_ctrl_profiles-1str-ovlp_2nt_ci20.png ; 2012-07-02.203348 $RSAT/perl-scripts/oligo-analysis -v 1 -quick -i $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/data/sequences/peak-motifs_ctrl_purged_ml30_mis0.fasta -format fasta -return occ,freq -2str -noov -seqtype dna -l 6 -o $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/oligos_6nt_vs_ctrl/peak-motifs_oligos_bg_from_ctrl_6nt-2str-noov.tab ; 2012-07-02.203348 $RSAT/perl-scripts/oligo-analysis -v 1 -quick -i $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/data/sequences/peak-motifs_ctrl_purged_ml30_mis0.fasta -format fasta -return occ,freq -2str -noov -seqtype dna -l 7 -o $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/oligos_7nt_vs_ctrl/peak-motifs_oligos_bg_from_ctrl_7nt-2str-noov.tab ; 2012-07-02.203350 time ($RSAT/perl-scripts/oligo-analysis -v 1 -quick -i $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/data/sequences/peak-motifs_test_purged_ml30_mis0.fasta -format fasta -sort -lth ratio 1 -lth occ_sig 0 -uth rank 50 -return occ,proba,rank -2str -noov -seqtype dna -l 6 -expfreq $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/oligos_6nt_vs_ctrl/peak-motifs_oligos_bg_from_ctrl_6nt-2str-noov.tab -pseudo 0.01 -o $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/oligos_6nt_vs_ctrl/peak-motifs_oligos-2str-noov_6nt_vs_ctrl.tab) >& $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/oligos_6nt_vs_ctrl/peak-motifs_oligos-2str-noov_6nt_vs_ctrl.tab_time.txt ; 2012-07-02.203351 time ($RSAT/perl-scripts/matrix-from-patterns -v 1 -seq $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/data/sequences/peak-motifs_test.fasta -pl $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/oligos_6nt_vs_ctrl/peak-motifs_oligos-2str-noov_6nt_vs_ctrl.tab -bgfile $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt -toppat 50 -max_asmb_nb 5 -subst 1 -prefix oligos_6nt_vs_ctrl -flanks 2 -collect_method matrix-scan-quick -logo -o $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/oligos_6nt_vs_ctrl/peak-motifs_oligos-2str-noov_6nt_vs_ctrl_pssm) >& $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/oligos_6nt_vs_ctrl/peak-motifs_oligos-2str-noov_6nt_vs_ctrl_pssm_time.txt ; 2012-07-02.203409 time ($RSAT/perl-scripts/oligo-analysis -v 1 -quick -i $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/data/sequences/peak-motifs_test_purged_ml30_mis0.fasta -format fasta -sort -lth ratio 1 -lth occ_sig 0 -uth rank 50 -return occ,proba,rank -2str -noov -seqtype dna -l 7 -expfreq $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/oligos_7nt_vs_ctrl/peak-motifs_oligos_bg_from_ctrl_7nt-2str-noov.tab -pseudo 0.01 -o $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/oligos_7nt_vs_ctrl/peak-motifs_oligos-2str-noov_7nt_vs_ctrl.tab) >& $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/oligos_7nt_vs_ctrl/peak-motifs_oligos-2str-noov_7nt_vs_ctrl.tab_time.txt ; 2012-07-02.203412 time ($RSAT/perl-scripts/matrix-from-patterns -v 1 -seq $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/data/sequences/peak-motifs_test.fasta -pl $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/oligos_7nt_vs_ctrl/peak-motifs_oligos-2str-noov_7nt_vs_ctrl.tab -bgfile $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt -toppat 50 -max_asmb_nb 5 -subst 1 -prefix oligos_7nt_vs_ctrl -flanks 2 -collect_method matrix-scan-quick -logo -o $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/oligos_7nt_vs_ctrl/peak-motifs_oligos-2str-noov_7nt_vs_ctrl_pssm) >& $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/oligos_7nt_vs_ctrl/peak-motifs_oligos-2str-noov_7nt_vs_ctrl_pssm_time.txt ; 2012-07-02.203429 time ($RSAT/perl-scripts/compare-scores -v 1 -i $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/oligos_6nt_vs_ctrl/peak-motifs_oligos-2str-noov_6nt_vs_ctrl.tab -sc1 8 -suppress $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/oligos_6nt_vs_ctrl/ -i $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/oligos_7nt_vs_ctrl/peak-motifs_oligos-2str-noov_7nt_vs_ctrl.tab -sc2 8 -suppress $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/oligos_7nt_vs_ctrl/ -ic 1 -lc -null . -suppress peak-motifs_ -suppress '.tab' | $RSAT/perl-scripts/row-stats -after 1 -sort -o $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/merged_words/peak-motifs_merged_words.tab) >& $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/merged_words/peak-motifs_merged_words.tab_time.txt ; 2012-07-02.203429 $RSAT/perl-scripts/text-to-html -i $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/merged_words/peak-motifs_merged_words.tab -o $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/merged_words/peak-motifs_merged_words.html ; 2012-07-02.203430 $RSAT/perl-scripts/draw-heatmap -min 0 -max 10 -out_format png -col_width 40 -rownames -gradient fire -row_height 16 -i $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/merged_words/peak-motifs_merged_words.tab -o $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/merged_words/peak-motifs_merged_words_heatmap.png ; 2012-07-02.203430 rm -f $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/peak-motifs_motifs_discovered.tf; cat $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/oligos_6nt_vs_ctrl/peak-motifs_oligos-2str-noov_6nt_vs_ctrl_pssm_count_matrices.tf >> $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/peak-motifs_motifs_discovered.tf; cat $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/oligos_7nt_vs_ctrl/peak-motifs_oligos-2str-noov_7nt_vs_ctrl_pssm_count_matrices.tf >> $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/peak-motifs_motifs_discovered.tf ; 2012-07-02.203430 $RSAT/perl-scripts/convert-matrix -v 0 -i $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_6nt_vs_ctrl_m1/peak-motifs_oligos_6nt_vs_ctrl_m1.tf -from transfac -to tab -return counts -o $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_6nt_vs_ctrl_m1/peak-motifs_oligos_6nt_vs_ctrl_m1.tab ; 2012-07-02.203430 $RSAT/perl-scripts/convert-matrix -v 0 -i $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_6nt_vs_ctrl_m2/peak-motifs_oligos_6nt_vs_ctrl_m2.tf -from transfac -to tab -return counts -o $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_6nt_vs_ctrl_m2/peak-motifs_oligos_6nt_vs_ctrl_m2.tab ; 2012-07-02.203430 $RSAT/perl-scripts/convert-matrix -v 0 -i $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_6nt_vs_ctrl_m3/peak-motifs_oligos_6nt_vs_ctrl_m3.tf -from transfac -to tab -return counts -o $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_6nt_vs_ctrl_m3/peak-motifs_oligos_6nt_vs_ctrl_m3.tab ; 2012-07-02.203430 $RSAT/perl-scripts/convert-matrix -v 0 -i $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_6nt_vs_ctrl_m4/peak-motifs_oligos_6nt_vs_ctrl_m4.tf -from transfac -to tab -return counts -o $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_6nt_vs_ctrl_m4/peak-motifs_oligos_6nt_vs_ctrl_m4.tab ; 2012-07-02.203431 $RSAT/perl-scripts/convert-matrix -v 0 -i $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_6nt_vs_ctrl_m5/peak-motifs_oligos_6nt_vs_ctrl_m5.tf -from transfac -to tab -return counts -o $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_6nt_vs_ctrl_m5/peak-motifs_oligos_6nt_vs_ctrl_m5.tab ; 2012-07-02.203431 $RSAT/perl-scripts/convert-matrix -v 0 -i $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_7nt_vs_ctrl_m1/peak-motifs_oligos_7nt_vs_ctrl_m1.tf -from transfac -to tab -return counts -o $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_7nt_vs_ctrl_m1/peak-motifs_oligos_7nt_vs_ctrl_m1.tab ; 2012-07-02.203431 $RSAT/perl-scripts/convert-matrix -v 0 -i $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_7nt_vs_ctrl_m2/peak-motifs_oligos_7nt_vs_ctrl_m2.tf -from transfac -to tab -return counts -o $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_7nt_vs_ctrl_m2/peak-motifs_oligos_7nt_vs_ctrl_m2.tab ; 2012-07-02.203431 $RSAT/perl-scripts/convert-matrix -v 0 -i $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_7nt_vs_ctrl_m3/peak-motifs_oligos_7nt_vs_ctrl_m3.tf -from transfac -to tab -return counts -o $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_7nt_vs_ctrl_m3/peak-motifs_oligos_7nt_vs_ctrl_m3.tab ; 2012-07-02.203431 $RSAT/perl-scripts/convert-matrix -v 0 -i $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_7nt_vs_ctrl_m4/peak-motifs_oligos_7nt_vs_ctrl_m4.tf -from transfac -to tab -return counts -o $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_7nt_vs_ctrl_m4/peak-motifs_oligos_7nt_vs_ctrl_m4.tab ; 2012-07-02.203431 $RSAT/perl-scripts/convert-matrix -v 0 -i $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_7nt_vs_ctrl_m5/peak-motifs_oligos_7nt_vs_ctrl_m5.tf -from transfac -to tab -return counts -o $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_7nt_vs_ctrl_m5/peak-motifs_oligos_7nt_vs_ctrl_m5.tab ; 2012-07-02.203432 $RSAT/perl-scripts/compare-matrices -v 1 -format transfac -file $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/peak-motifs_motifs_discovered.tf -distinct -mode matches -DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.75 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,logoDP,NIcor,NsEucl,SSD,NSW,match_rank,width,strand,offset,consensus,alignments_1ton -sort Ncor -o $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/peak-motifs_motifs_disco_compa.tab; $RSAT/perl-scripts/text-to-html -i $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/peak-motifs_motifs_disco_compa.tab -o $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/peak-motifs_motifs_disco_compa.html ; 2012-07-02.203435 $RSAT/perl-scripts/convert-graph -i $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/peak-motifs_motifs_disco_compa.tab -ewidth -ecolors fire -layout spring -from tab -to gml -scol 3 -tcol 4 -wcol 5 -o $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/peak-motifs_motifs_disco_compa.gml ; 2012-07-02.203435 $RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_6nt_vs_ctrl_m1/peak-motifs_oligos_6nt_vs_ctrl_m1.tf -format2 tf -file2 $RSAT/public_html/data/motif_databases/JASPAR/jaspar_core_vertebrates_2009_10.tf -mode matches -DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.75 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,logoDP,NIcor,NsEucl,SSD,NSW,match_rank,width,strand,offset,consensus,alignments_1ton -sort Ncor -o $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_6nt_vs_ctrl_m1/peak-motifs_oligos_6nt_vs_ctrl_m1_vs_db_jaspar_core_vertebrates ; 2012-07-02.203437 $RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_6nt_vs_ctrl_m2/peak-motifs_oligos_6nt_vs_ctrl_m2.tf -format2 tf -file2 $RSAT/public_html/data/motif_databases/JASPAR/jaspar_core_vertebrates_2009_10.tf -mode matches -DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.75 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,logoDP,NIcor,NsEucl,SSD,NSW,match_rank,width,strand,offset,consensus,alignments_1ton -sort Ncor -o $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_6nt_vs_ctrl_m2/peak-motifs_oligos_6nt_vs_ctrl_m2_vs_db_jaspar_core_vertebrates ; 2012-07-02.203440 $RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_6nt_vs_ctrl_m3/peak-motifs_oligos_6nt_vs_ctrl_m3.tf -format2 tf -file2 $RSAT/public_html/data/motif_databases/JASPAR/jaspar_core_vertebrates_2009_10.tf -mode matches -DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.75 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,logoDP,NIcor,NsEucl,SSD,NSW,match_rank,width,strand,offset,consensus,alignments_1ton -sort Ncor -o $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_6nt_vs_ctrl_m3/peak-motifs_oligos_6nt_vs_ctrl_m3_vs_db_jaspar_core_vertebrates ; 2012-07-02.203441 $RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_6nt_vs_ctrl_m4/peak-motifs_oligos_6nt_vs_ctrl_m4.tf -format2 tf -file2 $RSAT/public_html/data/motif_databases/JASPAR/jaspar_core_vertebrates_2009_10.tf -mode matches -DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.75 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,logoDP,NIcor,NsEucl,SSD,NSW,match_rank,width,strand,offset,consensus,alignments_1ton -sort Ncor -o $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_6nt_vs_ctrl_m4/peak-motifs_oligos_6nt_vs_ctrl_m4_vs_db_jaspar_core_vertebrates ; 2012-07-02.203443 $RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_6nt_vs_ctrl_m5/peak-motifs_oligos_6nt_vs_ctrl_m5.tf -format2 tf -file2 $RSAT/public_html/data/motif_databases/JASPAR/jaspar_core_vertebrates_2009_10.tf -mode matches -DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.75 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,logoDP,NIcor,NsEucl,SSD,NSW,match_rank,width,strand,offset,consensus,alignments_1ton -sort Ncor -o $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_6nt_vs_ctrl_m5/peak-motifs_oligos_6nt_vs_ctrl_m5_vs_db_jaspar_core_vertebrates ; 2012-07-02.203445 $RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_7nt_vs_ctrl_m1/peak-motifs_oligos_7nt_vs_ctrl_m1.tf -format2 tf -file2 $RSAT/public_html/data/motif_databases/JASPAR/jaspar_core_vertebrates_2009_10.tf -mode matches -DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.75 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,logoDP,NIcor,NsEucl,SSD,NSW,match_rank,width,strand,offset,consensus,alignments_1ton -sort Ncor -o $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_7nt_vs_ctrl_m1/peak-motifs_oligos_7nt_vs_ctrl_m1_vs_db_jaspar_core_vertebrates ; 2012-07-02.203448 $RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_7nt_vs_ctrl_m2/peak-motifs_oligos_7nt_vs_ctrl_m2.tf -format2 tf -file2 $RSAT/public_html/data/motif_databases/JASPAR/jaspar_core_vertebrates_2009_10.tf -mode matches -DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.75 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,logoDP,NIcor,NsEucl,SSD,NSW,match_rank,width,strand,offset,consensus,alignments_1ton -sort Ncor -o $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_7nt_vs_ctrl_m2/peak-motifs_oligos_7nt_vs_ctrl_m2_vs_db_jaspar_core_vertebrates ; 2012-07-02.203450 $RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_7nt_vs_ctrl_m3/peak-motifs_oligos_7nt_vs_ctrl_m3.tf -format2 tf -file2 $RSAT/public_html/data/motif_databases/JASPAR/jaspar_core_vertebrates_2009_10.tf -mode matches -DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.75 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,logoDP,NIcor,NsEucl,SSD,NSW,match_rank,width,strand,offset,consensus,alignments_1ton -sort Ncor -o $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_7nt_vs_ctrl_m3/peak-motifs_oligos_7nt_vs_ctrl_m3_vs_db_jaspar_core_vertebrates ; 2012-07-02.203452 $RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_7nt_vs_ctrl_m4/peak-motifs_oligos_7nt_vs_ctrl_m4.tf -format2 tf -file2 $RSAT/public_html/data/motif_databases/JASPAR/jaspar_core_vertebrates_2009_10.tf -mode matches -DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.75 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,logoDP,NIcor,NsEucl,SSD,NSW,match_rank,width,strand,offset,consensus,alignments_1ton -sort Ncor -o $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_7nt_vs_ctrl_m4/peak-motifs_oligos_7nt_vs_ctrl_m4_vs_db_jaspar_core_vertebrates ; 2012-07-02.203454 $RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_7nt_vs_ctrl_m5/peak-motifs_oligos_7nt_vs_ctrl_m5.tf -format2 tf -file2 $RSAT/public_html/data/motif_databases/JASPAR/jaspar_core_vertebrates_2009_10.tf -mode matches -DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.75 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,logoDP,NIcor,NsEucl,SSD,NSW,match_rank,width,strand,offset,consensus,alignments_1ton -sort Ncor -o $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_7nt_vs_ctrl_m5/peak-motifs_oligos_7nt_vs_ctrl_m5_vs_db_jaspar_core_vertebrates ; 2012-07-02.203456 time ($RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/peak-motifs_motifs_discovered.tf -format2 tf -file2 $RSAT/public_html/data/motif_databases/JASPAR/jaspar_core_vertebrates_2009_10.tf -mode matches -DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.75 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,logoDP,NIcor,NsEucl,SSD,NSW,match_rank,width,strand,offset,consensus,alignments_1ton -sort Ncor -o $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_vs_db/peak-motifs_motifs_vs_db_jaspar_core_vertebrates.tab) >& $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_vs_db/peak-motifs_motifs_vs_db_jaspar_core_vertebrates.tab_time.txt ; 2012-07-02.203512 $RSAT/perl-scripts/convert-graph -i $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_vs_db/peak-motifs_motifs_vs_db_jaspar_core_vertebrates.tab -ewidth -ecolors fire -layout spring -from tab -to gml -scol 3 -tcol 4 -wcol 5 -o $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_vs_db/peak-motifs_motifs_vs_db_jaspar_core_vertebrates.gml ; 2012-07-02.203512 $RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_6nt_vs_ctrl_m1/peak-motifs_oligos_6nt_vs_ctrl_m1.tf -format2 tf -file2 $RSAT/public_html/data/motif_databases/JASPAR/jaspar_pbm_mouse_2009_10.tf -mode matches -DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.75 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,logoDP,NIcor,NsEucl,SSD,NSW,match_rank,width,strand,offset,consensus,alignments_1ton -sort Ncor -o $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_6nt_vs_ctrl_m1/peak-motifs_oligos_6nt_vs_ctrl_m1_vs_db_jaspar_pbm_mouse ; 2012-07-02.203516 $RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_6nt_vs_ctrl_m2/peak-motifs_oligos_6nt_vs_ctrl_m2.tf -format2 tf -file2 $RSAT/public_html/data/motif_databases/JASPAR/jaspar_pbm_mouse_2009_10.tf -mode matches -DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.75 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,logoDP,NIcor,NsEucl,SSD,NSW,match_rank,width,strand,offset,consensus,alignments_1ton -sort Ncor -o $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_6nt_vs_ctrl_m2/peak-motifs_oligos_6nt_vs_ctrl_m2_vs_db_jaspar_pbm_mouse ; 2012-07-02.203519 $RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_6nt_vs_ctrl_m3/peak-motifs_oligos_6nt_vs_ctrl_m3.tf -format2 tf -file2 $RSAT/public_html/data/motif_databases/JASPAR/jaspar_pbm_mouse_2009_10.tf -mode matches -DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.75 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,logoDP,NIcor,NsEucl,SSD,NSW,match_rank,width,strand,offset,consensus,alignments_1ton -sort Ncor -o $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_6nt_vs_ctrl_m3/peak-motifs_oligos_6nt_vs_ctrl_m3_vs_db_jaspar_pbm_mouse ; 2012-07-02.203522 $RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_6nt_vs_ctrl_m4/peak-motifs_oligos_6nt_vs_ctrl_m4.tf -format2 tf -file2 $RSAT/public_html/data/motif_databases/JASPAR/jaspar_pbm_mouse_2009_10.tf -mode matches -DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.75 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,logoDP,NIcor,NsEucl,SSD,NSW,match_rank,width,strand,offset,consensus,alignments_1ton -sort Ncor -o $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_6nt_vs_ctrl_m4/peak-motifs_oligos_6nt_vs_ctrl_m4_vs_db_jaspar_pbm_mouse ; 2012-07-02.203525 $RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_6nt_vs_ctrl_m5/peak-motifs_oligos_6nt_vs_ctrl_m5.tf -format2 tf -file2 $RSAT/public_html/data/motif_databases/JASPAR/jaspar_pbm_mouse_2009_10.tf -mode matches -DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.75 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,logoDP,NIcor,NsEucl,SSD,NSW,match_rank,width,strand,offset,consensus,alignments_1ton -sort Ncor -o $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_6nt_vs_ctrl_m5/peak-motifs_oligos_6nt_vs_ctrl_m5_vs_db_jaspar_pbm_mouse ; 2012-07-02.203528 $RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_7nt_vs_ctrl_m1/peak-motifs_oligos_7nt_vs_ctrl_m1.tf -format2 tf -file2 $RSAT/public_html/data/motif_databases/JASPAR/jaspar_pbm_mouse_2009_10.tf -mode matches -DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.75 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,logoDP,NIcor,NsEucl,SSD,NSW,match_rank,width,strand,offset,consensus,alignments_1ton -sort Ncor -o $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_7nt_vs_ctrl_m1/peak-motifs_oligos_7nt_vs_ctrl_m1_vs_db_jaspar_pbm_mouse ; 2012-07-02.203531 $RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_7nt_vs_ctrl_m2/peak-motifs_oligos_7nt_vs_ctrl_m2.tf -format2 tf -file2 $RSAT/public_html/data/motif_databases/JASPAR/jaspar_pbm_mouse_2009_10.tf -mode matches -DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.75 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,logoDP,NIcor,NsEucl,SSD,NSW,match_rank,width,strand,offset,consensus,alignments_1ton -sort Ncor -o $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_7nt_vs_ctrl_m2/peak-motifs_oligos_7nt_vs_ctrl_m2_vs_db_jaspar_pbm_mouse ; 2012-07-02.203535 $RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_7nt_vs_ctrl_m3/peak-motifs_oligos_7nt_vs_ctrl_m3.tf -format2 tf -file2 $RSAT/public_html/data/motif_databases/JASPAR/jaspar_pbm_mouse_2009_10.tf -mode matches -DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.75 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,logoDP,NIcor,NsEucl,SSD,NSW,match_rank,width,strand,offset,consensus,alignments_1ton -sort Ncor -o $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_7nt_vs_ctrl_m3/peak-motifs_oligos_7nt_vs_ctrl_m3_vs_db_jaspar_pbm_mouse ; 2012-07-02.203538 $RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_7nt_vs_ctrl_m4/peak-motifs_oligos_7nt_vs_ctrl_m4.tf -format2 tf -file2 $RSAT/public_html/data/motif_databases/JASPAR/jaspar_pbm_mouse_2009_10.tf -mode matches -DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.75 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,logoDP,NIcor,NsEucl,SSD,NSW,match_rank,width,strand,offset,consensus,alignments_1ton -sort Ncor -o $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_7nt_vs_ctrl_m4/peak-motifs_oligos_7nt_vs_ctrl_m4_vs_db_jaspar_pbm_mouse ; 2012-07-02.203541 $RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_7nt_vs_ctrl_m5/peak-motifs_oligos_7nt_vs_ctrl_m5.tf -format2 tf -file2 $RSAT/public_html/data/motif_databases/JASPAR/jaspar_pbm_mouse_2009_10.tf -mode matches -DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.75 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,logoDP,NIcor,NsEucl,SSD,NSW,match_rank,width,strand,offset,consensus,alignments_1ton -sort Ncor -o $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_7nt_vs_ctrl_m5/peak-motifs_oligos_7nt_vs_ctrl_m5_vs_db_jaspar_pbm_mouse ; 2012-07-02.203544 time ($RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/peak-motifs_motifs_discovered.tf -format2 tf -file2 $RSAT/public_html/data/motif_databases/JASPAR/jaspar_pbm_mouse_2009_10.tf -mode matches -DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.75 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,logoDP,NIcor,NsEucl,SSD,NSW,match_rank,width,strand,offset,consensus,alignments_1ton -sort Ncor -o $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_vs_db/peak-motifs_motifs_vs_db_jaspar_pbm_mouse.tab) >& $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_vs_db/peak-motifs_motifs_vs_db_jaspar_pbm_mouse.tab_time.txt ; 2012-07-02.203608 $RSAT/perl-scripts/convert-graph -i $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_vs_db/peak-motifs_motifs_vs_db_jaspar_pbm_mouse.tab -ewidth -ecolors fire -layout spring -from tab -to gml -scol 3 -tcol 4 -wcol 5 -o $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_vs_db/peak-motifs_motifs_vs_db_jaspar_pbm_mouse.gml ; 2012-07-02.203609 $RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_6nt_vs_ctrl_m1/peak-motifs_oligos_6nt_vs_ctrl_m1.tf -format2 tf -file2 $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/peak-motifs_custom_motif_db.tf -mode matches -DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.75 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,logoDP,NIcor,NsEucl,SSD,NSW,match_rank,width,strand,offset,consensus,alignments_1ton -sort Ncor -o $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_6nt_vs_ctrl_m1/peak-motifs_oligos_6nt_vs_ctrl_m1_vs_db_custom_motif_collection ; 2012-07-02.203621 $RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_6nt_vs_ctrl_m2/peak-motifs_oligos_6nt_vs_ctrl_m2.tf -format2 tf -file2 $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/peak-motifs_custom_motif_db.tf -mode matches -DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.75 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,logoDP,NIcor,NsEucl,SSD,NSW,match_rank,width,strand,offset,consensus,alignments_1ton -sort Ncor -o $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_6nt_vs_ctrl_m2/peak-motifs_oligos_6nt_vs_ctrl_m2_vs_db_custom_motif_collection ; 2012-07-02.203633 $RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_6nt_vs_ctrl_m3/peak-motifs_oligos_6nt_vs_ctrl_m3.tf -format2 tf -file2 $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/peak-motifs_custom_motif_db.tf -mode matches -DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.75 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,logoDP,NIcor,NsEucl,SSD,NSW,match_rank,width,strand,offset,consensus,alignments_1ton -sort Ncor -o $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_6nt_vs_ctrl_m3/peak-motifs_oligos_6nt_vs_ctrl_m3_vs_db_custom_motif_collection ; 2012-07-02.203643 $RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_6nt_vs_ctrl_m4/peak-motifs_oligos_6nt_vs_ctrl_m4.tf -format2 tf -file2 $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/peak-motifs_custom_motif_db.tf -mode matches -DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.75 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,logoDP,NIcor,NsEucl,SSD,NSW,match_rank,width,strand,offset,consensus,alignments_1ton -sort Ncor -o $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_6nt_vs_ctrl_m4/peak-motifs_oligos_6nt_vs_ctrl_m4_vs_db_custom_motif_collection ; 2012-07-02.203653 $RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_6nt_vs_ctrl_m5/peak-motifs_oligos_6nt_vs_ctrl_m5.tf -format2 tf -file2 $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/peak-motifs_custom_motif_db.tf -mode matches -DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.75 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,logoDP,NIcor,NsEucl,SSD,NSW,match_rank,width,strand,offset,consensus,alignments_1ton -sort Ncor -o $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_6nt_vs_ctrl_m5/peak-motifs_oligos_6nt_vs_ctrl_m5_vs_db_custom_motif_collection ; 2012-07-02.203705 $RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_7nt_vs_ctrl_m1/peak-motifs_oligos_7nt_vs_ctrl_m1.tf -format2 tf -file2 $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/peak-motifs_custom_motif_db.tf -mode matches -DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.75 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,logoDP,NIcor,NsEucl,SSD,NSW,match_rank,width,strand,offset,consensus,alignments_1ton -sort Ncor -o $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_7nt_vs_ctrl_m1/peak-motifs_oligos_7nt_vs_ctrl_m1_vs_db_custom_motif_collection ; 2012-07-02.203717 $RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_7nt_vs_ctrl_m2/peak-motifs_oligos_7nt_vs_ctrl_m2.tf -format2 tf -file2 $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/peak-motifs_custom_motif_db.tf -mode matches -DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.75 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,logoDP,NIcor,NsEucl,SSD,NSW,match_rank,width,strand,offset,consensus,alignments_1ton -sort Ncor -o $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_7nt_vs_ctrl_m2/peak-motifs_oligos_7nt_vs_ctrl_m2_vs_db_custom_motif_collection ; 2012-07-02.203730 $RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_7nt_vs_ctrl_m3/peak-motifs_oligos_7nt_vs_ctrl_m3.tf -format2 tf -file2 $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/peak-motifs_custom_motif_db.tf -mode matches -DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.75 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,logoDP,NIcor,NsEucl,SSD,NSW,match_rank,width,strand,offset,consensus,alignments_1ton -sort Ncor -o $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_7nt_vs_ctrl_m3/peak-motifs_oligos_7nt_vs_ctrl_m3_vs_db_custom_motif_collection ; 2012-07-02.203741 $RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_7nt_vs_ctrl_m4/peak-motifs_oligos_7nt_vs_ctrl_m4.tf -format2 tf -file2 $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/peak-motifs_custom_motif_db.tf -mode matches -DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.75 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,logoDP,NIcor,NsEucl,SSD,NSW,match_rank,width,strand,offset,consensus,alignments_1ton -sort Ncor -o $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_7nt_vs_ctrl_m4/peak-motifs_oligos_7nt_vs_ctrl_m4_vs_db_custom_motif_collection ; 2012-07-02.203754 $RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_7nt_vs_ctrl_m5/peak-motifs_oligos_7nt_vs_ctrl_m5.tf -format2 tf -file2 $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/peak-motifs_custom_motif_db.tf -mode matches -DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.75 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,logoDP,NIcor,NsEucl,SSD,NSW,match_rank,width,strand,offset,consensus,alignments_1ton -sort Ncor -o $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_7nt_vs_ctrl_m5/peak-motifs_oligos_7nt_vs_ctrl_m5_vs_db_custom_motif_collection ; 2012-07-02.203805 time ($RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/peak-motifs_motifs_discovered.tf -format2 tf -file2 $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/peak-motifs_custom_motif_db.tf -mode matches -DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.75 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,logoDP,NIcor,NsEucl,SSD,NSW,match_rank,width,strand,offset,consensus,alignments_1ton -sort Ncor -o $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_vs_db/peak-motifs_motifs_vs_db_custom_motif_collection.tab) >& $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_vs_db/peak-motifs_motifs_vs_db_custom_motif_collection.tab_time.txt ; 2012-07-02.203940 $RSAT/perl-scripts/convert-graph -i $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_vs_db/peak-motifs_motifs_vs_db_custom_motif_collection.tab -ewidth -ecolors fire -layout spring -from tab -to gml -scol 3 -tcol 4 -wcol 5 -o $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_vs_db/peak-motifs_motifs_vs_db_custom_motif_collection.gml ; 2012-07-02.203946 time ($RSAT/perl-scripts/matrix-scan -quick -v 1 -seq_format fasta -i $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/data/sequences/peak-motifs_test.fasta -matrix_format transfac -m $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_6nt_vs_ctrl_m1/peak-motifs_oligos_6nt_vs_ctrl_m1.tf -bg_format inclusive -bgfile $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt -pseudo 1 -2str -decimals 1 -bg_pseudo 0.01 -n score -lth score 7.5 -origin center -return sites -o $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_6nt_vs_ctrl_m1/peak-motifs_oligos_6nt_vs_ctrl_m1_sites.tab) >& $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_6nt_vs_ctrl_m1/peak-motifs_oligos_6nt_vs_ctrl_m1_sites.tab_time.txt ; 2012-07-02.203947 $RSAT/perl-scripts/convert-features -from ft -i $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_6nt_vs_ctrl_m1/peak-motifs_oligos_6nt_vs_ctrl_m1_sites.tab -coord $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/data/sequences/peak-motifs_test_seqcoord.bed -origin center -to bed | sed '1s/^.*/track name="oligos_6nt_vs_ctrl_m1" description="RSAT peak-motifs p300_heart_versus_limb_Blow2010: oligos_6nt_vs_ctrl_m1" visibility=2 itemRgb="On" use_score=1 color=247,73,2/' > $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_6nt_vs_ctrl_m1/peak-motifs_oligos_6nt_vs_ctrl_m1_sites_genomic.bed ; 2012-07-02.203947 grep -v '^;' $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_6nt_vs_ctrl_m1/peak-motifs_oligos_6nt_vs_ctrl_m1_sites.tab | grep -v '^#' | awk '{print ($6+$5)/2}' | $RSAT/perl-scripts/classfreq -v 1 -ci 20 -o $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_6nt_vs_ctrl_m1/peak-motifs_oligos_6nt_vs_ctrl_m1_site_distrib.tab ; 2012-07-02.203947 $RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_6nt_vs_ctrl_m1/peak-motifs_oligos_6nt_vs_ctrl_m1_site_distrib.tab -lines -xcol 3 -ycol 4 -ysize 200 -ycol 4 -yleg1 'Number of sites' -xsize 800 -xcol 3 -xleg1 'Sequence position relative to peak center' -title1 'Predicted sites : oligos_6nt_vs_ctrl_m1' -o $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_6nt_vs_ctrl_m1/peak-motifs_oligos_6nt_vs_ctrl_m1_site_distrib.png ; 2012-07-02.203947 $RSAT/perl-scripts/contingency-table -i $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_6nt_vs_ctrl_m1/peak-motifs_oligos_6nt_vs_ctrl_m1_sites.tab | $RSAT/perl-scripts/classfreq -v 1 -ci 1 -o $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_6nt_vs_ctrl_m1/peak-motifs_oligos_6nt_vs_ctrl_m1_sites_per_peak.tab ; 2012-07-02.203947 $RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_6nt_vs_ctrl_m1/peak-motifs_oligos_6nt_vs_ctrl_m1_sites_per_peak.tab -lines -xcol 1 -ycol 4 -ysize 200 -ycol 4,6 -yleg1 'Number of peaks' -legend -xsize 400 -xcol 1 -xleg1 'Number of sites' -xgstep1 5 -xgstep2 1 -title1 'Nb Predicted sites : oligos_6nt_vs_ctrl_m1' -o $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_6nt_vs_ctrl_m1/peak-motifs_oligos_6nt_vs_ctrl_m1_sites_per_peak.png ; 2012-07-02.203948 time ($RSAT/perl-scripts/matrix-scan -v 3 -quick -seq_format fasta -i $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/data/sequences/peak-motifs_test.fasta -matrix_format transfac -m $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_6nt_vs_ctrl_m1/peak-motifs_oligos_6nt_vs_ctrl_m1.tf -pseudo 1 -2str -decimals 1 -bg_pseudo 0.01 -n score -lth score -5 -bginput -markov 2 -return distrib -return occ_proba -o $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_6nt_vs_ctrl_m1/peak-motifs_oligos_6nt_vs_ctrl_m1_scan_mkv2_enrichment.tab) >& $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_6nt_vs_ctrl_m1/peak-motifs_oligos_6nt_vs_ctrl_m1_scan_mkv2_enrichment.tab_time.txt ; 2012-07-02.203954 $RSAT/perl-scripts/XYgraph -i $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_6nt_vs_ctrl_m1/peak-motifs_oligos_6nt_vs_ctrl_m1_scan_mkv2_enrichment.tab -xcol 2 -xleg1 'Weight score' -xmin -5 -xsize 800 -xgstep1 5 -xgstep2 1 -hline red 100 -hline violet 0 -vline violet 5 -ycol 11 -yleg1 'Binomial significance of hit number' -ysize 400 -lines -o $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_6nt_vs_ctrl_m1/peak-motifs_oligos_6nt_vs_ctrl_m1_scan_mkv2_enrichment.png ; 2012-07-02.203954 time ($RSAT/perl-scripts/matrix-scan -quick -v 1 -seq_format fasta -i $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/data/sequences/peak-motifs_test.fasta -matrix_format transfac -m $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_6nt_vs_ctrl_m2/peak-motifs_oligos_6nt_vs_ctrl_m2.tf -bg_format inclusive -bgfile $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt -pseudo 1 -2str -decimals 1 -bg_pseudo 0.01 -n score -lth score 7.5 -origin center -return sites -o $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_6nt_vs_ctrl_m2/peak-motifs_oligos_6nt_vs_ctrl_m2_sites.tab) >& $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_6nt_vs_ctrl_m2/peak-motifs_oligos_6nt_vs_ctrl_m2_sites.tab_time.txt ; 2012-07-02.203955 $RSAT/perl-scripts/convert-features -from ft -i $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_6nt_vs_ctrl_m2/peak-motifs_oligos_6nt_vs_ctrl_m2_sites.tab -coord $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/data/sequences/peak-motifs_test_seqcoord.bed -origin center -to bed | sed '1s/^.*/track name="oligos_6nt_vs_ctrl_m2" description="RSAT peak-motifs p300_heart_versus_limb_Blow2010: oligos_6nt_vs_ctrl_m2" visibility=2 itemRgb="On" use_score=1 color=247,73,2/' > $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_6nt_vs_ctrl_m2/peak-motifs_oligos_6nt_vs_ctrl_m2_sites_genomic.bed ; 2012-07-02.203956 grep -v '^;' $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_6nt_vs_ctrl_m2/peak-motifs_oligos_6nt_vs_ctrl_m2_sites.tab | grep -v '^#' | awk '{print ($6+$5)/2}' | $RSAT/perl-scripts/classfreq -v 1 -ci 20 -o $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_6nt_vs_ctrl_m2/peak-motifs_oligos_6nt_vs_ctrl_m2_site_distrib.tab ; 2012-07-02.203956 $RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_6nt_vs_ctrl_m2/peak-motifs_oligos_6nt_vs_ctrl_m2_site_distrib.tab -lines -xcol 3 -ycol 4 -ysize 200 -ycol 4 -yleg1 'Number of sites' -xsize 800 -xcol 3 -xleg1 'Sequence position relative to peak center' -title1 'Predicted sites : oligos_6nt_vs_ctrl_m2' -o $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_6nt_vs_ctrl_m2/peak-motifs_oligos_6nt_vs_ctrl_m2_site_distrib.png ; 2012-07-02.203956 $RSAT/perl-scripts/contingency-table -i $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_6nt_vs_ctrl_m2/peak-motifs_oligos_6nt_vs_ctrl_m2_sites.tab | $RSAT/perl-scripts/classfreq -v 1 -ci 1 -o $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_6nt_vs_ctrl_m2/peak-motifs_oligos_6nt_vs_ctrl_m2_sites_per_peak.tab ; 2012-07-02.203956 $RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_6nt_vs_ctrl_m2/peak-motifs_oligos_6nt_vs_ctrl_m2_sites_per_peak.tab -lines -xcol 1 -ycol 4 -ysize 200 -ycol 4,6 -yleg1 'Number of peaks' -legend -xsize 400 -xcol 1 -xleg1 'Number of sites' -xgstep1 5 -xgstep2 1 -title1 'Nb Predicted sites : oligos_6nt_vs_ctrl_m2' -o $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_6nt_vs_ctrl_m2/peak-motifs_oligos_6nt_vs_ctrl_m2_sites_per_peak.png ; 2012-07-02.203956 time ($RSAT/perl-scripts/matrix-scan -v 3 -quick -seq_format fasta -i $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/data/sequences/peak-motifs_test.fasta -matrix_format transfac -m $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_6nt_vs_ctrl_m2/peak-motifs_oligos_6nt_vs_ctrl_m2.tf -pseudo 1 -2str -decimals 1 -bg_pseudo 0.01 -n score -lth score -5 -bginput -markov 2 -return distrib -return occ_proba -o $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_6nt_vs_ctrl_m2/peak-motifs_oligos_6nt_vs_ctrl_m2_scan_mkv2_enrichment.tab) >& $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_6nt_vs_ctrl_m2/peak-motifs_oligos_6nt_vs_ctrl_m2_scan_mkv2_enrichment.tab_time.txt ; 2012-07-02.204002 $RSAT/perl-scripts/XYgraph -i $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_6nt_vs_ctrl_m2/peak-motifs_oligos_6nt_vs_ctrl_m2_scan_mkv2_enrichment.tab -xcol 2 -xleg1 'Weight score' -xmin -5 -xsize 800 -xgstep1 5 -xgstep2 1 -hline red 100 -hline violet 0 -vline violet 5 -ycol 11 -yleg1 'Binomial significance of hit number' -ysize 400 -lines -o $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_6nt_vs_ctrl_m2/peak-motifs_oligos_6nt_vs_ctrl_m2_scan_mkv2_enrichment.png ; 2012-07-02.204002 time ($RSAT/perl-scripts/matrix-scan -quick -v 1 -seq_format fasta -i $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/data/sequences/peak-motifs_test.fasta -matrix_format transfac -m $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_6nt_vs_ctrl_m3/peak-motifs_oligos_6nt_vs_ctrl_m3.tf -bg_format inclusive -bgfile $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt -pseudo 1 -2str -decimals 1 -bg_pseudo 0.01 -n score -lth score 7.5 -origin center -return sites -o $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_6nt_vs_ctrl_m3/peak-motifs_oligos_6nt_vs_ctrl_m3_sites.tab) >& $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_6nt_vs_ctrl_m3/peak-motifs_oligos_6nt_vs_ctrl_m3_sites.tab_time.txt ; 2012-07-02.204003 $RSAT/perl-scripts/convert-features -from ft -i $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_6nt_vs_ctrl_m3/peak-motifs_oligos_6nt_vs_ctrl_m3_sites.tab -coord $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/data/sequences/peak-motifs_test_seqcoord.bed -origin center -to bed | sed '1s/^.*/track name="oligos_6nt_vs_ctrl_m3" description="RSAT peak-motifs p300_heart_versus_limb_Blow2010: oligos_6nt_vs_ctrl_m3" visibility=2 itemRgb="On" use_score=1 color=247,73,2/' > $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_6nt_vs_ctrl_m3/peak-motifs_oligos_6nt_vs_ctrl_m3_sites_genomic.bed ; 2012-07-02.204003 grep -v '^;' $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_6nt_vs_ctrl_m3/peak-motifs_oligos_6nt_vs_ctrl_m3_sites.tab | grep -v '^#' | awk '{print ($6+$5)/2}' | $RSAT/perl-scripts/classfreq -v 1 -ci 20 -o $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_6nt_vs_ctrl_m3/peak-motifs_oligos_6nt_vs_ctrl_m3_site_distrib.tab ; 2012-07-02.204004 $RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_6nt_vs_ctrl_m3/peak-motifs_oligos_6nt_vs_ctrl_m3_site_distrib.tab -lines -xcol 3 -ycol 4 -ysize 200 -ycol 4 -yleg1 'Number of sites' -xsize 800 -xcol 3 -xleg1 'Sequence position relative to peak center' -title1 'Predicted sites : oligos_6nt_vs_ctrl_m3' -o $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_6nt_vs_ctrl_m3/peak-motifs_oligos_6nt_vs_ctrl_m3_site_distrib.png ; 2012-07-02.204004 $RSAT/perl-scripts/contingency-table -i $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_6nt_vs_ctrl_m3/peak-motifs_oligos_6nt_vs_ctrl_m3_sites.tab | $RSAT/perl-scripts/classfreq -v 1 -ci 1 -o $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_6nt_vs_ctrl_m3/peak-motifs_oligos_6nt_vs_ctrl_m3_sites_per_peak.tab ; 2012-07-02.204004 $RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_6nt_vs_ctrl_m3/peak-motifs_oligos_6nt_vs_ctrl_m3_sites_per_peak.tab -lines -xcol 1 -ycol 4 -ysize 200 -ycol 4,6 -yleg1 'Number of peaks' -legend -xsize 400 -xcol 1 -xleg1 'Number of sites' -xgstep1 5 -xgstep2 1 -title1 'Nb Predicted sites : oligos_6nt_vs_ctrl_m3' -o $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_6nt_vs_ctrl_m3/peak-motifs_oligos_6nt_vs_ctrl_m3_sites_per_peak.png ; 2012-07-02.204004 time ($RSAT/perl-scripts/matrix-scan -v 3 -quick -seq_format fasta -i $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/data/sequences/peak-motifs_test.fasta -matrix_format transfac -m $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_6nt_vs_ctrl_m3/peak-motifs_oligos_6nt_vs_ctrl_m3.tf -pseudo 1 -2str -decimals 1 -bg_pseudo 0.01 -n score -lth score -5 -bginput -markov 2 -return distrib -return occ_proba -o $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_6nt_vs_ctrl_m3/peak-motifs_oligos_6nt_vs_ctrl_m3_scan_mkv2_enrichment.tab) >& $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_6nt_vs_ctrl_m3/peak-motifs_oligos_6nt_vs_ctrl_m3_scan_mkv2_enrichment.tab_time.txt ; 2012-07-02.204011 $RSAT/perl-scripts/XYgraph -i $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_6nt_vs_ctrl_m3/peak-motifs_oligos_6nt_vs_ctrl_m3_scan_mkv2_enrichment.tab -xcol 2 -xleg1 'Weight score' -xmin -5 -xsize 800 -xgstep1 5 -xgstep2 1 -hline red 100 -hline violet 0 -vline violet 5 -ycol 11 -yleg1 'Binomial significance of hit number' -ysize 400 -lines -o $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_6nt_vs_ctrl_m3/peak-motifs_oligos_6nt_vs_ctrl_m3_scan_mkv2_enrichment.png ; 2012-07-02.204011 time ($RSAT/perl-scripts/matrix-scan -quick -v 1 -seq_format fasta -i $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/data/sequences/peak-motifs_test.fasta -matrix_format transfac -m $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_6nt_vs_ctrl_m4/peak-motifs_oligos_6nt_vs_ctrl_m4.tf -bg_format inclusive -bgfile $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt -pseudo 1 -2str -decimals 1 -bg_pseudo 0.01 -n score -lth score 7.5 -origin center -return sites -o $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_6nt_vs_ctrl_m4/peak-motifs_oligos_6nt_vs_ctrl_m4_sites.tab) >& $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_6nt_vs_ctrl_m4/peak-motifs_oligos_6nt_vs_ctrl_m4_sites.tab_time.txt ; 2012-07-02.204012 $RSAT/perl-scripts/convert-features -from ft -i $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_6nt_vs_ctrl_m4/peak-motifs_oligos_6nt_vs_ctrl_m4_sites.tab -coord $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/data/sequences/peak-motifs_test_seqcoord.bed -origin center -to bed | sed '1s/^.*/track name="oligos_6nt_vs_ctrl_m4" description="RSAT peak-motifs p300_heart_versus_limb_Blow2010: oligos_6nt_vs_ctrl_m4" visibility=2 itemRgb="On" use_score=1 color=247,73,2/' > $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_6nt_vs_ctrl_m4/peak-motifs_oligos_6nt_vs_ctrl_m4_sites_genomic.bed ; 2012-07-02.204013 grep -v '^;' $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_6nt_vs_ctrl_m4/peak-motifs_oligos_6nt_vs_ctrl_m4_sites.tab | grep -v '^#' | awk '{print ($6+$5)/2}' | $RSAT/perl-scripts/classfreq -v 1 -ci 20 -o $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_6nt_vs_ctrl_m4/peak-motifs_oligos_6nt_vs_ctrl_m4_site_distrib.tab ; 2012-07-02.204013 $RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_6nt_vs_ctrl_m4/peak-motifs_oligos_6nt_vs_ctrl_m4_site_distrib.tab -lines -xcol 3 -ycol 4 -ysize 200 -ycol 4 -yleg1 'Number of sites' -xsize 800 -xcol 3 -xleg1 'Sequence position relative to peak center' -title1 'Predicted sites : oligos_6nt_vs_ctrl_m4' -o $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_6nt_vs_ctrl_m4/peak-motifs_oligos_6nt_vs_ctrl_m4_site_distrib.png ; 2012-07-02.204013 $RSAT/perl-scripts/contingency-table -i $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_6nt_vs_ctrl_m4/peak-motifs_oligos_6nt_vs_ctrl_m4_sites.tab | $RSAT/perl-scripts/classfreq -v 1 -ci 1 -o $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_6nt_vs_ctrl_m4/peak-motifs_oligos_6nt_vs_ctrl_m4_sites_per_peak.tab ; 2012-07-02.204013 $RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_6nt_vs_ctrl_m4/peak-motifs_oligos_6nt_vs_ctrl_m4_sites_per_peak.tab -lines -xcol 1 -ycol 4 -ysize 200 -ycol 4,6 -yleg1 'Number of peaks' -legend -xsize 400 -xcol 1 -xleg1 'Number of sites' -xgstep1 5 -xgstep2 1 -title1 'Nb Predicted sites : oligos_6nt_vs_ctrl_m4' -o $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_6nt_vs_ctrl_m4/peak-motifs_oligos_6nt_vs_ctrl_m4_sites_per_peak.png ; 2012-07-02.204013 time ($RSAT/perl-scripts/matrix-scan -v 3 -quick -seq_format fasta -i $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/data/sequences/peak-motifs_test.fasta -matrix_format transfac -m $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_6nt_vs_ctrl_m4/peak-motifs_oligos_6nt_vs_ctrl_m4.tf -pseudo 1 -2str -decimals 1 -bg_pseudo 0.01 -n score -lth score -5 -bginput -markov 2 -return distrib -return occ_proba -o $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_6nt_vs_ctrl_m4/peak-motifs_oligos_6nt_vs_ctrl_m4_scan_mkv2_enrichment.tab) >& $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_6nt_vs_ctrl_m4/peak-motifs_oligos_6nt_vs_ctrl_m4_scan_mkv2_enrichment.tab_time.txt ; 2012-07-02.204017 $RSAT/perl-scripts/XYgraph -i $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_6nt_vs_ctrl_m4/peak-motifs_oligos_6nt_vs_ctrl_m4_scan_mkv2_enrichment.tab -xcol 2 -xleg1 'Weight score' -xmin -5 -xsize 800 -xgstep1 5 -xgstep2 1 -hline red 100 -hline violet 0 -vline violet 5 -ycol 11 -yleg1 'Binomial significance of hit number' -ysize 400 -lines -o $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_6nt_vs_ctrl_m4/peak-motifs_oligos_6nt_vs_ctrl_m4_scan_mkv2_enrichment.png ; 2012-07-02.204018 time ($RSAT/perl-scripts/matrix-scan -quick -v 1 -seq_format fasta -i $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/data/sequences/peak-motifs_test.fasta -matrix_format transfac -m $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_6nt_vs_ctrl_m5/peak-motifs_oligos_6nt_vs_ctrl_m5.tf -bg_format inclusive -bgfile $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt -pseudo 1 -2str -decimals 1 -bg_pseudo 0.01 -n score -lth score 7.5 -origin center -return sites -o $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_6nt_vs_ctrl_m5/peak-motifs_oligos_6nt_vs_ctrl_m5_sites.tab) >& $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_6nt_vs_ctrl_m5/peak-motifs_oligos_6nt_vs_ctrl_m5_sites.tab_time.txt ; 2012-07-02.204019 $RSAT/perl-scripts/convert-features -from ft -i $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_6nt_vs_ctrl_m5/peak-motifs_oligos_6nt_vs_ctrl_m5_sites.tab -coord $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/data/sequences/peak-motifs_test_seqcoord.bed -origin center -to bed | sed '1s/^.*/track name="oligos_6nt_vs_ctrl_m5" description="RSAT peak-motifs p300_heart_versus_limb_Blow2010: oligos_6nt_vs_ctrl_m5" visibility=2 itemRgb="On" use_score=1 color=247,73,2/' > $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_6nt_vs_ctrl_m5/peak-motifs_oligos_6nt_vs_ctrl_m5_sites_genomic.bed ; 2012-07-02.204019 grep -v '^;' $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_6nt_vs_ctrl_m5/peak-motifs_oligos_6nt_vs_ctrl_m5_sites.tab | grep -v '^#' | awk '{print ($6+$5)/2}' | $RSAT/perl-scripts/classfreq -v 1 -ci 20 -o $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_6nt_vs_ctrl_m5/peak-motifs_oligos_6nt_vs_ctrl_m5_site_distrib.tab ; 2012-07-02.204019 $RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_6nt_vs_ctrl_m5/peak-motifs_oligos_6nt_vs_ctrl_m5_site_distrib.tab -lines -xcol 3 -ycol 4 -ysize 200 -ycol 4 -yleg1 'Number of sites' -xsize 800 -xcol 3 -xleg1 'Sequence position relative to peak center' -title1 'Predicted sites : oligos_6nt_vs_ctrl_m5' -o $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_6nt_vs_ctrl_m5/peak-motifs_oligos_6nt_vs_ctrl_m5_site_distrib.png ; 2012-07-02.204019 $RSAT/perl-scripts/contingency-table -i $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_6nt_vs_ctrl_m5/peak-motifs_oligos_6nt_vs_ctrl_m5_sites.tab | $RSAT/perl-scripts/classfreq -v 1 -ci 1 -o $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_6nt_vs_ctrl_m5/peak-motifs_oligos_6nt_vs_ctrl_m5_sites_per_peak.tab ; 2012-07-02.204019 $RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_6nt_vs_ctrl_m5/peak-motifs_oligos_6nt_vs_ctrl_m5_sites_per_peak.tab -lines -xcol 1 -ycol 4 -ysize 200 -ycol 4,6 -yleg1 'Number of peaks' -legend -xsize 400 -xcol 1 -xleg1 'Number of sites' -xgstep1 5 -xgstep2 1 -title1 'Nb Predicted sites : oligos_6nt_vs_ctrl_m5' -o $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_6nt_vs_ctrl_m5/peak-motifs_oligos_6nt_vs_ctrl_m5_sites_per_peak.png ; 2012-07-02.204019 time ($RSAT/perl-scripts/matrix-scan -v 3 -quick -seq_format fasta -i $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/data/sequences/peak-motifs_test.fasta -matrix_format transfac -m $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_6nt_vs_ctrl_m5/peak-motifs_oligos_6nt_vs_ctrl_m5.tf -pseudo 1 -2str -decimals 1 -bg_pseudo 0.01 -n score -lth score -5 -bginput -markov 2 -return distrib -return occ_proba -o $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_6nt_vs_ctrl_m5/peak-motifs_oligos_6nt_vs_ctrl_m5_scan_mkv2_enrichment.tab) >& $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_6nt_vs_ctrl_m5/peak-motifs_oligos_6nt_vs_ctrl_m5_scan_mkv2_enrichment.tab_time.txt ; 2012-07-02.204025 $RSAT/perl-scripts/XYgraph -i $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_6nt_vs_ctrl_m5/peak-motifs_oligos_6nt_vs_ctrl_m5_scan_mkv2_enrichment.tab -xcol 2 -xleg1 'Weight score' -xmin -5 -xsize 800 -xgstep1 5 -xgstep2 1 -hline red 100 -hline violet 0 -vline violet 5 -ycol 11 -yleg1 'Binomial significance of hit number' -ysize 400 -lines -o $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_6nt_vs_ctrl_m5/peak-motifs_oligos_6nt_vs_ctrl_m5_scan_mkv2_enrichment.png ; 2012-07-02.204025 time ($RSAT/perl-scripts/matrix-scan -quick -v 1 -seq_format fasta -i $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/data/sequences/peak-motifs_test.fasta -matrix_format transfac -m $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_7nt_vs_ctrl_m1/peak-motifs_oligos_7nt_vs_ctrl_m1.tf -bg_format inclusive -bgfile $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt -pseudo 1 -2str -decimals 1 -bg_pseudo 0.01 -n score -lth score 7.5 -origin center -return sites -o $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_7nt_vs_ctrl_m1/peak-motifs_oligos_7nt_vs_ctrl_m1_sites.tab) >& $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_7nt_vs_ctrl_m1/peak-motifs_oligos_7nt_vs_ctrl_m1_sites.tab_time.txt ; 2012-07-02.204026 $RSAT/perl-scripts/convert-features -from ft -i $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_7nt_vs_ctrl_m1/peak-motifs_oligos_7nt_vs_ctrl_m1_sites.tab -coord $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/data/sequences/peak-motifs_test_seqcoord.bed -origin center -to bed | sed '1s/^.*/track name="oligos_7nt_vs_ctrl_m1" description="RSAT peak-motifs p300_heart_versus_limb_Blow2010: oligos_7nt_vs_ctrl_m1" visibility=2 itemRgb="On" use_score=1 color=247,73,2/' > $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_7nt_vs_ctrl_m1/peak-motifs_oligos_7nt_vs_ctrl_m1_sites_genomic.bed ; 2012-07-02.204027 grep -v '^;' $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_7nt_vs_ctrl_m1/peak-motifs_oligos_7nt_vs_ctrl_m1_sites.tab | grep -v '^#' | awk '{print ($6+$5)/2}' | $RSAT/perl-scripts/classfreq -v 1 -ci 20 -o $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_7nt_vs_ctrl_m1/peak-motifs_oligos_7nt_vs_ctrl_m1_site_distrib.tab ; 2012-07-02.204027 $RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_7nt_vs_ctrl_m1/peak-motifs_oligos_7nt_vs_ctrl_m1_site_distrib.tab -lines -xcol 3 -ycol 4 -ysize 200 -ycol 4 -yleg1 'Number of sites' -xsize 800 -xcol 3 -xleg1 'Sequence position relative to peak center' -title1 'Predicted sites : oligos_7nt_vs_ctrl_m1' -o $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_7nt_vs_ctrl_m1/peak-motifs_oligos_7nt_vs_ctrl_m1_site_distrib.png ; 2012-07-02.204027 $RSAT/perl-scripts/contingency-table -i $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_7nt_vs_ctrl_m1/peak-motifs_oligos_7nt_vs_ctrl_m1_sites.tab | $RSAT/perl-scripts/classfreq -v 1 -ci 1 -o $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_7nt_vs_ctrl_m1/peak-motifs_oligos_7nt_vs_ctrl_m1_sites_per_peak.tab ; 2012-07-02.204027 $RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_7nt_vs_ctrl_m1/peak-motifs_oligos_7nt_vs_ctrl_m1_sites_per_peak.tab -lines -xcol 1 -ycol 4 -ysize 200 -ycol 4,6 -yleg1 'Number of peaks' -legend -xsize 400 -xcol 1 -xleg1 'Number of sites' -xgstep1 5 -xgstep2 1 -title1 'Nb Predicted sites : oligos_7nt_vs_ctrl_m1' -o $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_7nt_vs_ctrl_m1/peak-motifs_oligos_7nt_vs_ctrl_m1_sites_per_peak.png ; 2012-07-02.204027 time ($RSAT/perl-scripts/matrix-scan -v 3 -quick -seq_format fasta -i $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/data/sequences/peak-motifs_test.fasta -matrix_format transfac -m $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_7nt_vs_ctrl_m1/peak-motifs_oligos_7nt_vs_ctrl_m1.tf -pseudo 1 -2str -decimals 1 -bg_pseudo 0.01 -n score -lth score -5 -bginput -markov 2 -return distrib -return occ_proba -o $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_7nt_vs_ctrl_m1/peak-motifs_oligos_7nt_vs_ctrl_m1_scan_mkv2_enrichment.tab) >& $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_7nt_vs_ctrl_m1/peak-motifs_oligos_7nt_vs_ctrl_m1_scan_mkv2_enrichment.tab_time.txt ; 2012-07-02.204036 $RSAT/perl-scripts/XYgraph -i $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_7nt_vs_ctrl_m1/peak-motifs_oligos_7nt_vs_ctrl_m1_scan_mkv2_enrichment.tab -xcol 2 -xleg1 'Weight score' -xmin -5 -xsize 800 -xgstep1 5 -xgstep2 1 -hline red 100 -hline violet 0 -vline violet 5 -ycol 11 -yleg1 'Binomial significance of hit number' -ysize 400 -lines -o $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_7nt_vs_ctrl_m1/peak-motifs_oligos_7nt_vs_ctrl_m1_scan_mkv2_enrichment.png ; 2012-07-02.204036 time ($RSAT/perl-scripts/matrix-scan -quick -v 1 -seq_format fasta -i $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/data/sequences/peak-motifs_test.fasta -matrix_format transfac -m $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_7nt_vs_ctrl_m2/peak-motifs_oligos_7nt_vs_ctrl_m2.tf -bg_format inclusive -bgfile $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt -pseudo 1 -2str -decimals 1 -bg_pseudo 0.01 -n score -lth score 7.5 -origin center -return sites -o $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_7nt_vs_ctrl_m2/peak-motifs_oligos_7nt_vs_ctrl_m2_sites.tab) >& $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_7nt_vs_ctrl_m2/peak-motifs_oligos_7nt_vs_ctrl_m2_sites.tab_time.txt ; 2012-07-02.204037 $RSAT/perl-scripts/convert-features -from ft -i $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_7nt_vs_ctrl_m2/peak-motifs_oligos_7nt_vs_ctrl_m2_sites.tab -coord $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/data/sequences/peak-motifs_test_seqcoord.bed -origin center -to bed | sed '1s/^.*/track name="oligos_7nt_vs_ctrl_m2" description="RSAT peak-motifs p300_heart_versus_limb_Blow2010: oligos_7nt_vs_ctrl_m2" visibility=2 itemRgb="On" use_score=1 color=247,73,2/' > $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_7nt_vs_ctrl_m2/peak-motifs_oligos_7nt_vs_ctrl_m2_sites_genomic.bed ; 2012-07-02.204038 grep -v '^;' $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_7nt_vs_ctrl_m2/peak-motifs_oligos_7nt_vs_ctrl_m2_sites.tab | grep -v '^#' | awk '{print ($6+$5)/2}' | $RSAT/perl-scripts/classfreq -v 1 -ci 20 -o $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_7nt_vs_ctrl_m2/peak-motifs_oligos_7nt_vs_ctrl_m2_site_distrib.tab ; 2012-07-02.204038 $RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_7nt_vs_ctrl_m2/peak-motifs_oligos_7nt_vs_ctrl_m2_site_distrib.tab -lines -xcol 3 -ycol 4 -ysize 200 -ycol 4 -yleg1 'Number of sites' -xsize 800 -xcol 3 -xleg1 'Sequence position relative to peak center' -title1 'Predicted sites : oligos_7nt_vs_ctrl_m2' -o $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_7nt_vs_ctrl_m2/peak-motifs_oligos_7nt_vs_ctrl_m2_site_distrib.png ; 2012-07-02.204038 $RSAT/perl-scripts/contingency-table -i $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_7nt_vs_ctrl_m2/peak-motifs_oligos_7nt_vs_ctrl_m2_sites.tab | $RSAT/perl-scripts/classfreq -v 1 -ci 1 -o $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_7nt_vs_ctrl_m2/peak-motifs_oligos_7nt_vs_ctrl_m2_sites_per_peak.tab ; 2012-07-02.204038 $RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_7nt_vs_ctrl_m2/peak-motifs_oligos_7nt_vs_ctrl_m2_sites_per_peak.tab -lines -xcol 1 -ycol 4 -ysize 200 -ycol 4,6 -yleg1 'Number of peaks' -legend -xsize 400 -xcol 1 -xleg1 'Number of sites' -xgstep1 5 -xgstep2 1 -title1 'Nb Predicted sites : oligos_7nt_vs_ctrl_m2' -o $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_7nt_vs_ctrl_m2/peak-motifs_oligos_7nt_vs_ctrl_m2_sites_per_peak.png ; 2012-07-02.204038 time ($RSAT/perl-scripts/matrix-scan -v 3 -quick -seq_format fasta -i $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/data/sequences/peak-motifs_test.fasta -matrix_format transfac -m $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_7nt_vs_ctrl_m2/peak-motifs_oligos_7nt_vs_ctrl_m2.tf -pseudo 1 -2str -decimals 1 -bg_pseudo 0.01 -n score -lth score -5 -bginput -markov 2 -return distrib -return occ_proba -o $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_7nt_vs_ctrl_m2/peak-motifs_oligos_7nt_vs_ctrl_m2_scan_mkv2_enrichment.tab) >& $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_7nt_vs_ctrl_m2/peak-motifs_oligos_7nt_vs_ctrl_m2_scan_mkv2_enrichment.tab_time.txt ; 2012-07-02.204046 $RSAT/perl-scripts/XYgraph -i $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_7nt_vs_ctrl_m2/peak-motifs_oligos_7nt_vs_ctrl_m2_scan_mkv2_enrichment.tab -xcol 2 -xleg1 'Weight score' -xmin -5 -xsize 800 -xgstep1 5 -xgstep2 1 -hline red 100 -hline violet 0 -vline violet 5 -ycol 11 -yleg1 'Binomial significance of hit number' -ysize 400 -lines -o $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_7nt_vs_ctrl_m2/peak-motifs_oligos_7nt_vs_ctrl_m2_scan_mkv2_enrichment.png ; 2012-07-02.204046 time ($RSAT/perl-scripts/matrix-scan -quick -v 1 -seq_format fasta -i $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/data/sequences/peak-motifs_test.fasta -matrix_format transfac -m $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_7nt_vs_ctrl_m3/peak-motifs_oligos_7nt_vs_ctrl_m3.tf -bg_format inclusive -bgfile $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt -pseudo 1 -2str -decimals 1 -bg_pseudo 0.01 -n score -lth score 7.5 -origin center -return sites -o $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_7nt_vs_ctrl_m3/peak-motifs_oligos_7nt_vs_ctrl_m3_sites.tab) >& $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_7nt_vs_ctrl_m3/peak-motifs_oligos_7nt_vs_ctrl_m3_sites.tab_time.txt ; 2012-07-02.204047 $RSAT/perl-scripts/convert-features -from ft -i $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_7nt_vs_ctrl_m3/peak-motifs_oligos_7nt_vs_ctrl_m3_sites.tab -coord $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/data/sequences/peak-motifs_test_seqcoord.bed -origin center -to bed | sed '1s/^.*/track name="oligos_7nt_vs_ctrl_m3" description="RSAT peak-motifs p300_heart_versus_limb_Blow2010: oligos_7nt_vs_ctrl_m3" visibility=2 itemRgb="On" use_score=1 color=247,73,2/' > $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_7nt_vs_ctrl_m3/peak-motifs_oligos_7nt_vs_ctrl_m3_sites_genomic.bed ; 2012-07-02.204047 grep -v '^;' $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_7nt_vs_ctrl_m3/peak-motifs_oligos_7nt_vs_ctrl_m3_sites.tab | grep -v '^#' | awk '{print ($6+$5)/2}' | $RSAT/perl-scripts/classfreq -v 1 -ci 20 -o $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_7nt_vs_ctrl_m3/peak-motifs_oligos_7nt_vs_ctrl_m3_site_distrib.tab ; 2012-07-02.204047 $RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_7nt_vs_ctrl_m3/peak-motifs_oligos_7nt_vs_ctrl_m3_site_distrib.tab -lines -xcol 3 -ycol 4 -ysize 200 -ycol 4 -yleg1 'Number of sites' -xsize 800 -xcol 3 -xleg1 'Sequence position relative to peak center' -title1 'Predicted sites : oligos_7nt_vs_ctrl_m3' -o $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_7nt_vs_ctrl_m3/peak-motifs_oligos_7nt_vs_ctrl_m3_site_distrib.png ; 2012-07-02.204047 $RSAT/perl-scripts/contingency-table -i $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_7nt_vs_ctrl_m3/peak-motifs_oligos_7nt_vs_ctrl_m3_sites.tab | $RSAT/perl-scripts/classfreq -v 1 -ci 1 -o $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_7nt_vs_ctrl_m3/peak-motifs_oligos_7nt_vs_ctrl_m3_sites_per_peak.tab ; 2012-07-02.204048 $RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_7nt_vs_ctrl_m3/peak-motifs_oligos_7nt_vs_ctrl_m3_sites_per_peak.tab -lines -xcol 1 -ycol 4 -ysize 200 -ycol 4,6 -yleg1 'Number of peaks' -legend -xsize 400 -xcol 1 -xleg1 'Number of sites' -xgstep1 5 -xgstep2 1 -title1 'Nb Predicted sites : oligos_7nt_vs_ctrl_m3' -o $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_7nt_vs_ctrl_m3/peak-motifs_oligos_7nt_vs_ctrl_m3_sites_per_peak.png ; 2012-07-02.204048 time ($RSAT/perl-scripts/matrix-scan -v 3 -quick -seq_format fasta -i $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/data/sequences/peak-motifs_test.fasta -matrix_format transfac -m $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_7nt_vs_ctrl_m3/peak-motifs_oligos_7nt_vs_ctrl_m3.tf -pseudo 1 -2str -decimals 1 -bg_pseudo 0.01 -n score -lth score -5 -bginput -markov 2 -return distrib -return occ_proba -o $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_7nt_vs_ctrl_m3/peak-motifs_oligos_7nt_vs_ctrl_m3_scan_mkv2_enrichment.tab) >& $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_7nt_vs_ctrl_m3/peak-motifs_oligos_7nt_vs_ctrl_m3_scan_mkv2_enrichment.tab_time.txt ; 2012-07-02.204056 $RSAT/perl-scripts/XYgraph -i $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_7nt_vs_ctrl_m3/peak-motifs_oligos_7nt_vs_ctrl_m3_scan_mkv2_enrichment.tab -xcol 2 -xleg1 'Weight score' -xmin -5 -xsize 800 -xgstep1 5 -xgstep2 1 -hline red 100 -hline violet 0 -vline violet 5 -ycol 11 -yleg1 'Binomial significance of hit number' -ysize 400 -lines -o $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_7nt_vs_ctrl_m3/peak-motifs_oligos_7nt_vs_ctrl_m3_scan_mkv2_enrichment.png ; 2012-07-02.204056 time ($RSAT/perl-scripts/matrix-scan -quick -v 1 -seq_format fasta -i $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/data/sequences/peak-motifs_test.fasta -matrix_format transfac -m $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_7nt_vs_ctrl_m4/peak-motifs_oligos_7nt_vs_ctrl_m4.tf -bg_format inclusive -bgfile $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt -pseudo 1 -2str -decimals 1 -bg_pseudo 0.01 -n score -lth score 7.5 -origin center -return sites -o $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_7nt_vs_ctrl_m4/peak-motifs_oligos_7nt_vs_ctrl_m4_sites.tab) >& $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_7nt_vs_ctrl_m4/peak-motifs_oligos_7nt_vs_ctrl_m4_sites.tab_time.txt ; 2012-07-02.204058 $RSAT/perl-scripts/convert-features -from ft -i $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_7nt_vs_ctrl_m4/peak-motifs_oligos_7nt_vs_ctrl_m4_sites.tab -coord $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/data/sequences/peak-motifs_test_seqcoord.bed -origin center -to bed | sed '1s/^.*/track name="oligos_7nt_vs_ctrl_m4" description="RSAT peak-motifs p300_heart_versus_limb_Blow2010: oligos_7nt_vs_ctrl_m4" visibility=2 itemRgb="On" use_score=1 color=247,73,2/' > $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_7nt_vs_ctrl_m4/peak-motifs_oligos_7nt_vs_ctrl_m4_sites_genomic.bed ; 2012-07-02.204058 grep -v '^;' $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_7nt_vs_ctrl_m4/peak-motifs_oligos_7nt_vs_ctrl_m4_sites.tab | grep -v '^#' | awk '{print ($6+$5)/2}' | $RSAT/perl-scripts/classfreq -v 1 -ci 20 -o $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_7nt_vs_ctrl_m4/peak-motifs_oligos_7nt_vs_ctrl_m4_site_distrib.tab ; 2012-07-02.204058 $RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_7nt_vs_ctrl_m4/peak-motifs_oligos_7nt_vs_ctrl_m4_site_distrib.tab -lines -xcol 3 -ycol 4 -ysize 200 -ycol 4 -yleg1 'Number of sites' -xsize 800 -xcol 3 -xleg1 'Sequence position relative to peak center' -title1 'Predicted sites : oligos_7nt_vs_ctrl_m4' -o $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_7nt_vs_ctrl_m4/peak-motifs_oligos_7nt_vs_ctrl_m4_site_distrib.png ; 2012-07-02.204058 $RSAT/perl-scripts/contingency-table -i $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_7nt_vs_ctrl_m4/peak-motifs_oligos_7nt_vs_ctrl_m4_sites.tab | $RSAT/perl-scripts/classfreq -v 1 -ci 1 -o $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_7nt_vs_ctrl_m4/peak-motifs_oligos_7nt_vs_ctrl_m4_sites_per_peak.tab ; 2012-07-02.204058 $RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_7nt_vs_ctrl_m4/peak-motifs_oligos_7nt_vs_ctrl_m4_sites_per_peak.tab -lines -xcol 1 -ycol 4 -ysize 200 -ycol 4,6 -yleg1 'Number of peaks' -legend -xsize 400 -xcol 1 -xleg1 'Number of sites' -xgstep1 5 -xgstep2 1 -title1 'Nb Predicted sites : oligos_7nt_vs_ctrl_m4' -o $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_7nt_vs_ctrl_m4/peak-motifs_oligos_7nt_vs_ctrl_m4_sites_per_peak.png ; 2012-07-02.204059 time ($RSAT/perl-scripts/matrix-scan -v 3 -quick -seq_format fasta -i $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/data/sequences/peak-motifs_test.fasta -matrix_format transfac -m $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_7nt_vs_ctrl_m4/peak-motifs_oligos_7nt_vs_ctrl_m4.tf -pseudo 1 -2str -decimals 1 -bg_pseudo 0.01 -n score -lth score -5 -bginput -markov 2 -return distrib -return occ_proba -o $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_7nt_vs_ctrl_m4/peak-motifs_oligos_7nt_vs_ctrl_m4_scan_mkv2_enrichment.tab) >& $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_7nt_vs_ctrl_m4/peak-motifs_oligos_7nt_vs_ctrl_m4_scan_mkv2_enrichment.tab_time.txt ; 2012-07-02.204106 $RSAT/perl-scripts/XYgraph -i $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_7nt_vs_ctrl_m4/peak-motifs_oligos_7nt_vs_ctrl_m4_scan_mkv2_enrichment.tab -xcol 2 -xleg1 'Weight score' -xmin -5 -xsize 800 -xgstep1 5 -xgstep2 1 -hline red 100 -hline violet 0 -vline violet 5 -ycol 11 -yleg1 'Binomial significance of hit number' -ysize 400 -lines -o $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_7nt_vs_ctrl_m4/peak-motifs_oligos_7nt_vs_ctrl_m4_scan_mkv2_enrichment.png ; 2012-07-02.204106 time ($RSAT/perl-scripts/matrix-scan -quick -v 1 -seq_format fasta -i $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/data/sequences/peak-motifs_test.fasta -matrix_format transfac -m $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_7nt_vs_ctrl_m5/peak-motifs_oligos_7nt_vs_ctrl_m5.tf -bg_format inclusive -bgfile $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt -pseudo 1 -2str -decimals 1 -bg_pseudo 0.01 -n score -lth score 7.5 -origin center -return sites -o $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_7nt_vs_ctrl_m5/peak-motifs_oligos_7nt_vs_ctrl_m5_sites.tab) >& $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_7nt_vs_ctrl_m5/peak-motifs_oligos_7nt_vs_ctrl_m5_sites.tab_time.txt ; 2012-07-02.204107 $RSAT/perl-scripts/convert-features -from ft -i $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_7nt_vs_ctrl_m5/peak-motifs_oligos_7nt_vs_ctrl_m5_sites.tab -coord $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/data/sequences/peak-motifs_test_seqcoord.bed -origin center -to bed | sed '1s/^.*/track name="oligos_7nt_vs_ctrl_m5" description="RSAT peak-motifs p300_heart_versus_limb_Blow2010: oligos_7nt_vs_ctrl_m5" visibility=2 itemRgb="On" use_score=1 color=247,73,2/' > $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_7nt_vs_ctrl_m5/peak-motifs_oligos_7nt_vs_ctrl_m5_sites_genomic.bed ; 2012-07-02.204107 grep -v '^;' $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_7nt_vs_ctrl_m5/peak-motifs_oligos_7nt_vs_ctrl_m5_sites.tab | grep -v '^#' | awk '{print ($6+$5)/2}' | $RSAT/perl-scripts/classfreq -v 1 -ci 20 -o $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_7nt_vs_ctrl_m5/peak-motifs_oligos_7nt_vs_ctrl_m5_site_distrib.tab ; 2012-07-02.204107 $RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_7nt_vs_ctrl_m5/peak-motifs_oligos_7nt_vs_ctrl_m5_site_distrib.tab -lines -xcol 3 -ycol 4 -ysize 200 -ycol 4 -yleg1 'Number of sites' -xsize 800 -xcol 3 -xleg1 'Sequence position relative to peak center' -title1 'Predicted sites : oligos_7nt_vs_ctrl_m5' -o $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_7nt_vs_ctrl_m5/peak-motifs_oligos_7nt_vs_ctrl_m5_site_distrib.png ; 2012-07-02.204108 $RSAT/perl-scripts/contingency-table -i $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_7nt_vs_ctrl_m5/peak-motifs_oligos_7nt_vs_ctrl_m5_sites.tab | $RSAT/perl-scripts/classfreq -v 1 -ci 1 -o $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_7nt_vs_ctrl_m5/peak-motifs_oligos_7nt_vs_ctrl_m5_sites_per_peak.tab ; 2012-07-02.204108 $RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_7nt_vs_ctrl_m5/peak-motifs_oligos_7nt_vs_ctrl_m5_sites_per_peak.tab -lines -xcol 1 -ycol 4 -ysize 200 -ycol 4,6 -yleg1 'Number of peaks' -legend -xsize 400 -xcol 1 -xleg1 'Number of sites' -xgstep1 5 -xgstep2 1 -title1 'Nb Predicted sites : oligos_7nt_vs_ctrl_m5' -o $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_7nt_vs_ctrl_m5/peak-motifs_oligos_7nt_vs_ctrl_m5_sites_per_peak.png ; 2012-07-02.204108 time ($RSAT/perl-scripts/matrix-scan -v 3 -quick -seq_format fasta -i $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/data/sequences/peak-motifs_test.fasta -matrix_format transfac -m $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_7nt_vs_ctrl_m5/peak-motifs_oligos_7nt_vs_ctrl_m5.tf -pseudo 1 -2str -decimals 1 -bg_pseudo 0.01 -n score -lth score -5 -bginput -markov 2 -return distrib -return occ_proba -o $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_7nt_vs_ctrl_m5/peak-motifs_oligos_7nt_vs_ctrl_m5_scan_mkv2_enrichment.tab) >& $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_7nt_vs_ctrl_m5/peak-motifs_oligos_7nt_vs_ctrl_m5_scan_mkv2_enrichment.tab_time.txt ; 2012-07-02.204112 $RSAT/perl-scripts/XYgraph -i $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_7nt_vs_ctrl_m5/peak-motifs_oligos_7nt_vs_ctrl_m5_scan_mkv2_enrichment.tab -xcol 2 -xleg1 'Weight score' -xmin -5 -xsize 800 -xgstep1 5 -xgstep2 1 -hline red 100 -hline violet 0 -vline violet 5 -ycol 11 -yleg1 'Binomial significance of hit number' -ysize 400 -lines -o $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_7nt_vs_ctrl_m5/peak-motifs_oligos_7nt_vs_ctrl_m5_scan_mkv2_enrichment.png ; 2012-07-02.204112 cat $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_6nt_vs_ctrl_m1/peak-motifs_oligos_6nt_vs_ctrl_m1_sites.tab $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_6nt_vs_ctrl_m2/peak-motifs_oligos_6nt_vs_ctrl_m2_sites.tab $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_6nt_vs_ctrl_m3/peak-motifs_oligos_6nt_vs_ctrl_m3_sites.tab $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_6nt_vs_ctrl_m4/peak-motifs_oligos_6nt_vs_ctrl_m4_sites.tab $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_6nt_vs_ctrl_m5/peak-motifs_oligos_6nt_vs_ctrl_m5_sites.tab $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_7nt_vs_ctrl_m1/peak-motifs_oligos_7nt_vs_ctrl_m1_sites.tab $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_7nt_vs_ctrl_m2/peak-motifs_oligos_7nt_vs_ctrl_m2_sites.tab $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_7nt_vs_ctrl_m3/peak-motifs_oligos_7nt_vs_ctrl_m3_sites.tab $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_7nt_vs_ctrl_m4/peak-motifs_oligos_7nt_vs_ctrl_m4_sites.tab $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_7nt_vs_ctrl_m5/peak-motifs_oligos_7nt_vs_ctrl_m5_sites.tab $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_6nt_vs_ctrl_m1/peak-motifs_oligos_6nt_vs_ctrl_m1_sites.tab $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_6nt_vs_ctrl_m2/peak-motifs_oligos_6nt_vs_ctrl_m2_sites.tab $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_6nt_vs_ctrl_m3/peak-motifs_oligos_6nt_vs_ctrl_m3_sites.tab $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_6nt_vs_ctrl_m4/peak-motifs_oligos_6nt_vs_ctrl_m4_sites.tab $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_6nt_vs_ctrl_m5/peak-motifs_oligos_6nt_vs_ctrl_m5_sites.tab $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_7nt_vs_ctrl_m1/peak-motifs_oligos_7nt_vs_ctrl_m1_sites.tab $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_7nt_vs_ctrl_m2/peak-motifs_oligos_7nt_vs_ctrl_m2_sites.tab $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_7nt_vs_ctrl_m3/peak-motifs_oligos_7nt_vs_ctrl_m3_sites.tab $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_7nt_vs_ctrl_m4/peak-motifs_oligos_7nt_vs_ctrl_m4_sites.tab $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_7nt_vs_ctrl_m5/peak-motifs_oligos_7nt_vs_ctrl_m5_sites.tab $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_6nt_vs_ctrl_m1/peak-motifs_oligos_6nt_vs_ctrl_m1_sites.tab $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_6nt_vs_ctrl_m2/peak-motifs_oligos_6nt_vs_ctrl_m2_sites.tab $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_6nt_vs_ctrl_m3/peak-motifs_oligos_6nt_vs_ctrl_m3_sites.tab $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_6nt_vs_ctrl_m4/peak-motifs_oligos_6nt_vs_ctrl_m4_sites.tab $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_6nt_vs_ctrl_m5/peak-motifs_oligos_6nt_vs_ctrl_m5_sites.tab $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_7nt_vs_ctrl_m1/peak-motifs_oligos_7nt_vs_ctrl_m1_sites.tab $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_7nt_vs_ctrl_m2/peak-motifs_oligos_7nt_vs_ctrl_m2_sites.tab $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_7nt_vs_ctrl_m3/peak-motifs_oligos_7nt_vs_ctrl_m3_sites.tab $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_7nt_vs_ctrl_m4/peak-motifs_oligos_7nt_vs_ctrl_m4_sites.tab $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_7nt_vs_ctrl_m5/peak-motifs_oligos_7nt_vs_ctrl_m5_sites.tab > $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/sites/peak-motifs_all_motifs_seqcoord.tab ; 2012-07-02.204112 cat $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/data/sequences/peak-motifs_test_seqcoord.bed $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_6nt_vs_ctrl_m1/peak-motifs_oligos_6nt_vs_ctrl_m1_sites_genomic.bed $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_6nt_vs_ctrl_m2/peak-motifs_oligos_6nt_vs_ctrl_m2_sites_genomic.bed $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_6nt_vs_ctrl_m3/peak-motifs_oligos_6nt_vs_ctrl_m3_sites_genomic.bed $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_6nt_vs_ctrl_m4/peak-motifs_oligos_6nt_vs_ctrl_m4_sites_genomic.bed $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_6nt_vs_ctrl_m5/peak-motifs_oligos_6nt_vs_ctrl_m5_sites_genomic.bed $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_7nt_vs_ctrl_m1/peak-motifs_oligos_7nt_vs_ctrl_m1_sites_genomic.bed $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_7nt_vs_ctrl_m2/peak-motifs_oligos_7nt_vs_ctrl_m2_sites_genomic.bed $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_7nt_vs_ctrl_m3/peak-motifs_oligos_7nt_vs_ctrl_m3_sites_genomic.bed $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_7nt_vs_ctrl_m4/peak-motifs_oligos_7nt_vs_ctrl_m4_sites_genomic.bed $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_7nt_vs_ctrl_m5/peak-motifs_oligos_7nt_vs_ctrl_m5_sites_genomic.bed $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_6nt_vs_ctrl_m1/peak-motifs_oligos_6nt_vs_ctrl_m1_sites_genomic.bed $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_6nt_vs_ctrl_m2/peak-motifs_oligos_6nt_vs_ctrl_m2_sites_genomic.bed $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_6nt_vs_ctrl_m3/peak-motifs_oligos_6nt_vs_ctrl_m3_sites_genomic.bed $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_6nt_vs_ctrl_m4/peak-motifs_oligos_6nt_vs_ctrl_m4_sites_genomic.bed $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_6nt_vs_ctrl_m5/peak-motifs_oligos_6nt_vs_ctrl_m5_sites_genomic.bed $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_7nt_vs_ctrl_m1/peak-motifs_oligos_7nt_vs_ctrl_m1_sites_genomic.bed $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_7nt_vs_ctrl_m2/peak-motifs_oligos_7nt_vs_ctrl_m2_sites_genomic.bed $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_7nt_vs_ctrl_m3/peak-motifs_oligos_7nt_vs_ctrl_m3_sites_genomic.bed $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_7nt_vs_ctrl_m4/peak-motifs_oligos_7nt_vs_ctrl_m4_sites_genomic.bed $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_7nt_vs_ctrl_m5/peak-motifs_oligos_7nt_vs_ctrl_m5_sites_genomic.bed $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_6nt_vs_ctrl_m1/peak-motifs_oligos_6nt_vs_ctrl_m1_sites_genomic.bed $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_6nt_vs_ctrl_m2/peak-motifs_oligos_6nt_vs_ctrl_m2_sites_genomic.bed $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_6nt_vs_ctrl_m3/peak-motifs_oligos_6nt_vs_ctrl_m3_sites_genomic.bed $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_6nt_vs_ctrl_m4/peak-motifs_oligos_6nt_vs_ctrl_m4_sites_genomic.bed $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_6nt_vs_ctrl_m5/peak-motifs_oligos_6nt_vs_ctrl_m5_sites_genomic.bed $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_7nt_vs_ctrl_m1/peak-motifs_oligos_7nt_vs_ctrl_m1_sites_genomic.bed $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_7nt_vs_ctrl_m2/peak-motifs_oligos_7nt_vs_ctrl_m2_sites_genomic.bed $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_7nt_vs_ctrl_m3/peak-motifs_oligos_7nt_vs_ctrl_m3_sites_genomic.bed $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_7nt_vs_ctrl_m4/peak-motifs_oligos_7nt_vs_ctrl_m4_sites_genomic.bed $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_7nt_vs_ctrl_m5/peak-motifs_oligos_7nt_vs_ctrl_m5_sites_genomic.bed > $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/sites/peak-motifs_all_motifs_seqcoord.bed ; 2012-07-02.204115 $RSAT/perl-scripts/text-to-html -font variable -i $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/reports/peak-motifs_timelog.txt -o $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/reports/peak-motifs_timelog.html ; peak-motifs -v 1 -title p300_heart_versus_limb_Blow2010 -i $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/peak-motifspeak_seq -ctrl $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/peak-motifscontrol_seq -markov auto -disco oligos -nmotifs 5 -minol 6 -maxol 7 -2str -motif_db jaspar_core_vertebrates tf $RSAT/public_html/data/motif_databases/JASPAR/jaspar_core_vertebrates_2009_10.tf -motif_db jaspar_pbm_mouse tf $RSAT/public_html/data/motif_databases/JASPAR/jaspar_pbm_mouse_2009_10.tf -motif_db custom_motif_collection tf $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/peak-motifs_custom_motif_db.tf -source galaxy -task purge,seqlen,composition,disco,merge_words,collect_motifs,motifs_vs_motifs,timelog,archive,synthesis,motifs_vs_db,motifs_vs_db,scan -prefix peak-motifs -noov -img_format png -outdir $RSAT/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg ; Program version 1.234 ; Parameter values ; seq_format fasta ; img_format png ; ref_motifs_format transfac ; purge_match_length 30 ; purge_mismatches 0 ; profiles_ci 20 ; profiles_max_graphs 20 ; profiles_strand -1str ; profiles_oligo_lengths 1,2 ; profiles_noov -ovlp ; strand -2str ; disco_noov -noov ; oligo_min_len 6 ; oligo_max_len 7 ; patterns_max_rank 50 ; min_ratio 1 ; min_zscore 6 ; min_sig 0 ; oligo_min_mkv auto ; oligo_max_mkv auto ; positions_max_graphs 20 ; asmb_toppat 50 ; matrix_nmotifs 5 ; Input files ; ctrl_seq /home/rsat/rsa-tools/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/peak-motifscontrol_seq ; motif_db_custom_motif_collection /home/rsat/rsa-tools/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/peak-motifs_custom_motif_db.tf ; motif_db_jaspar_core_vertebrates /home/rsat/rsa-tools/public_html/data/motif_databases/JASPAR/jaspar_core_vertebrates_2009_10.tf ; motif_db_jaspar_pbm_mouse /home/rsat/rsa-tools/public_html/data/motif_databases/JASPAR/jaspar_pbm_mouse_2009_10.tf ; test_seq /home/rsat/rsa-tools/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/peak-motifspeak_seq ; Directories ; output /home/rsat/rsa-tools/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/ ; oligos_6nt_vs_ctrl_m1 /home/rsat/rsa-tools/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_6nt_vs_ctrl_m1/ ; oligos_6nt_vs_ctrl_m2 /home/rsat/rsa-tools/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_6nt_vs_ctrl_m2/ ; oligos_6nt_vs_ctrl_m3 /home/rsat/rsa-tools/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_6nt_vs_ctrl_m3/ ; oligos_6nt_vs_ctrl_m4 /home/rsat/rsa-tools/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_6nt_vs_ctrl_m4/ ; oligos_6nt_vs_ctrl_m5 /home/rsat/rsa-tools/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_6nt_vs_ctrl_m5/ ; oligos_7nt_vs_ctrl_m1 /home/rsat/rsa-tools/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_7nt_vs_ctrl_m1/ ; oligos_7nt_vs_ctrl_m2 /home/rsat/rsa-tools/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_7nt_vs_ctrl_m2/ ; oligos_7nt_vs_ctrl_m3 /home/rsat/rsa-tools/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_7nt_vs_ctrl_m3/ ; oligos_7nt_vs_ctrl_m4 /home/rsat/rsa-tools/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_7nt_vs_ctrl_m4/ ; oligos_7nt_vs_ctrl_m5 /home/rsat/rsa-tools/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_7nt_vs_ctrl_m5/ ; Output files ; 1nt_ctrl_freq /home/rsat/rsa-tools/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/composition/peak-motifs_ctrl_freq-1str-ovlp_1nt.tab ; 1nt_ctrl_heatmap /home/rsat/rsa-tools/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/composition/peak-motifs_ctrl_heatmap-1str-ovlp_1nt.png ; 1nt_ctrl_inclusive /home/rsat/rsa-tools/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/composition/peak-motifs_ctrl_inclusive-1str-ovlp_1nt.txt ; 1nt_ctrl_profiles /home/rsat/rsa-tools/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/composition/peak-motifs_ctrl_profiles-1str-ovlp_1nt_ci20.tab ; 1nt_ctrl_profiles_graph /home/rsat/rsa-tools/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/composition/peak-motifs_ctrl_profiles-1str-ovlp_1nt_ci20.png ; 1nt_ctrl_profiles_index /home/rsat/rsa-tools/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/composition/peak-motifs_ctrl_profiles-1str-ovlp_1nt_ci20_graph_index.html ; 1nt_ctrl_transitions /home/rsat/rsa-tools/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/composition/peak-motifs_ctrl_transitions-1str-ovlp_1nt.tab ; 1nt_test_freq /home/rsat/rsa-tools/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/composition/peak-motifs_test_freq-1str-ovlp_1nt.tab ; 1nt_test_heatmap /home/rsat/rsa-tools/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/composition/peak-motifs_test_heatmap-1str-ovlp_1nt.png ; 1nt_test_inclusive /home/rsat/rsa-tools/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/composition/peak-motifs_test_inclusive-1str-ovlp_1nt.txt ; 1nt_test_profiles /home/rsat/rsa-tools/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/composition/peak-motifs_test_profiles-1str-ovlp_1nt_ci20.tab ; 1nt_test_profiles_graph /home/rsat/rsa-tools/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/composition/peak-motifs_test_profiles-1str-ovlp_1nt_ci20.png ; 1nt_test_profiles_index /home/rsat/rsa-tools/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/composition/peak-motifs_test_profiles-1str-ovlp_1nt_ci20_graph_index.html ; 1nt_test_transitions /home/rsat/rsa-tools/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/composition/peak-motifs_test_transitions-1str-ovlp_1nt.tab ; 2nt_ctrl_freq /home/rsat/rsa-tools/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/composition/peak-motifs_ctrl_freq-1str-ovlp_2nt.tab ; 2nt_ctrl_heatmap /home/rsat/rsa-tools/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/composition/peak-motifs_ctrl_heatmap-1str-ovlp_2nt.png ; 2nt_ctrl_inclusive /home/rsat/rsa-tools/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/composition/peak-motifs_ctrl_inclusive-1str-ovlp_2nt.txt ; 2nt_ctrl_profiles /home/rsat/rsa-tools/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/composition/peak-motifs_ctrl_profiles-1str-ovlp_2nt_ci20.tab ; 2nt_ctrl_profiles_graph /home/rsat/rsa-tools/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/composition/peak-motifs_ctrl_profiles-1str-ovlp_2nt_ci20.png ; 2nt_ctrl_profiles_index /home/rsat/rsa-tools/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/composition/peak-motifs_ctrl_profiles-1str-ovlp_2nt_ci20_graph_index.html ; 2nt_ctrl_transitions /home/rsat/rsa-tools/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/composition/peak-motifs_ctrl_transitions-1str-ovlp_2nt.tab ; 2nt_test_freq /home/rsat/rsa-tools/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/composition/peak-motifs_test_freq-1str-ovlp_2nt.tab ; 2nt_test_heatmap /home/rsat/rsa-tools/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/composition/peak-motifs_test_heatmap-1str-ovlp_2nt.png ; 2nt_test_inclusive /home/rsat/rsa-tools/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt ; 2nt_test_profiles /home/rsat/rsa-tools/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/composition/peak-motifs_test_profiles-1str-ovlp_2nt_ci20.tab ; 2nt_test_profiles_graph /home/rsat/rsa-tools/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/composition/peak-motifs_test_profiles-1str-ovlp_2nt_ci20.png ; 2nt_test_profiles_index /home/rsat/rsa-tools/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/composition/peak-motifs_test_profiles-1str-ovlp_2nt_ci20_graph_index.html ; 2nt_test_transitions /home/rsat/rsa-tools/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/composition/peak-motifs_test_transitions-1str-ovlp_2nt.tab ; archive /home/rsat/rsa-tools/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/peak-motifs_archive.zip ; ctrl_converted /home/rsat/rsa-tools/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/data/sequences/peak-motifs_ctrl.fasta ; ctrl_purged /home/rsat/rsa-tools/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/data/sequences/peak-motifs_ctrl_purged_ml30_mis0.fasta ; ctrl_seqlen /home/rsat/rsa-tools/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/data/sequences/peak-motifs_ctrl_seqlen.tab ; ctrl_seqlen_distrib /home/rsat/rsa-tools/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/data/sequences/peak-motifs_ctrl_seqlen_distrib.tab ; ctrl_seqlen_distrib_graph /home/rsat/rsa-tools/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/data/sequences/peak-motifs_ctrl_seqlen_distrib.png ; links /home/rsat/rsa-tools/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/reports/peak-motifs_links.html ; log /home/rsat/rsa-tools/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/reports/peak-motifs_log.txt ; merged_sites /home/rsat/rsa-tools/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/sites/peak-motifs_all_motifs_seqcoord.tab ; merged_sites_bed /home/rsat/rsa-tools/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/sites/peak-motifs_all_motifs_seqcoord.bed ; merged_words /home/rsat/rsa-tools/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/merged_words/peak-motifs_merged_words.tab ; merged_words_heatmap /home/rsat/rsa-tools/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/merged_words/peak-motifs_merged_words_heatmap.png ; merged_words_html /home/rsat/rsa-tools/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/merged_words/peak-motifs_merged_words.html ; motifs_disco_compa /home/rsat/rsa-tools/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/peak-motifs_motifs_disco_compa.tab ; motifs_disco_compa_alignments_1ton /home/rsat/rsa-tools/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/peak-motifs_motifs_disco_compa_alignments_1ton.tab ; motifs_disco_compa_alignments_1ton_html /home/rsat/rsa-tools/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/peak-motifs_motifs_disco_compa_alignments_1ton.html ; motifs_disco_compa_gml /home/rsat/rsa-tools/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/peak-motifs_motifs_disco_compa.gml ; motifs_disco_compa_html 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/home/rsat/rsa-tools/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_6nt_vs_ctrl_m5/peak-motifs_oligos_6nt_vs_ctrl_m5_vs_db_jaspar_pbm_mouse.tab ; oligos_6nt_vs_ctrl_m5_vs_db_jaspar_pbm_mouse_html /home/rsat/rsa-tools/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_6nt_vs_ctrl_m5/peak-motifs_oligos_6nt_vs_ctrl_m5_vs_db_jaspar_pbm_mouse.html ; oligos_6nt_vs_ctrl_m5_vs_ref /home/rsat/rsa-tools/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_6nt_vs_ctrl_m5/peak-motifs_oligos_6nt_vs_ctrl_m5_vs_ref.tab ; oligos_6nt_vs_ctrl_m5_vs_ref_html /home/rsat/rsa-tools/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_6nt_vs_ctrl_m5/peak-motifs_oligos_6nt_vs_ctrl_m5_vs_ref.html ; oligos_6nt_vs_ctrl_pssm_counts 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/home/rsat/rsa-tools/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_7nt_vs_ctrl_m2/peak-motifs_oligos_7nt_vs_ctrl_m2_vs_db_jaspar_pbm_mouse.tab ; oligos_7nt_vs_ctrl_m2_vs_db_jaspar_pbm_mouse_html /home/rsat/rsa-tools/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_7nt_vs_ctrl_m2/peak-motifs_oligos_7nt_vs_ctrl_m2_vs_db_jaspar_pbm_mouse.html ; oligos_7nt_vs_ctrl_m2_vs_ref /home/rsat/rsa-tools/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_7nt_vs_ctrl_m2/peak-motifs_oligos_7nt_vs_ctrl_m2_vs_ref.tab ; oligos_7nt_vs_ctrl_m2_vs_ref_html /home/rsat/rsa-tools/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_7nt_vs_ctrl_m2/peak-motifs_oligos_7nt_vs_ctrl_m2_vs_ref.html ; oligos_7nt_vs_ctrl_m3_logo 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/home/rsat/rsa-tools/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_7nt_vs_ctrl_m5/peak-motifs_oligos_7nt_vs_ctrl_m5_site_distrib.png ; oligos_7nt_vs_ctrl_m5_pssm_sites /home/rsat/rsa-tools/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_7nt_vs_ctrl_m5/peak-motifs_oligos_7nt_vs_ctrl_m5_sites.tab ; oligos_7nt_vs_ctrl_m5_pssm_sites_genomic /home/rsat/rsa-tools/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_7nt_vs_ctrl_m5/peak-motifs_oligos_7nt_vs_ctrl_m5_sites_genomic.bed ; oligos_7nt_vs_ctrl_m5_pssm_sites_per_peak /home/rsat/rsa-tools/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_7nt_vs_ctrl_m5/peak-motifs_oligos_7nt_vs_ctrl_m5_sites_per_peak.tab ; oligos_7nt_vs_ctrl_m5_pssm_sites_per_peak_graph /home/rsat/rsa-tools/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_7nt_vs_ctrl_m5/peak-motifs_oligos_7nt_vs_ctrl_m5_sites_per_peak.png ; oligos_7nt_vs_ctrl_m5_tab /home/rsat/rsa-tools/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_7nt_vs_ctrl_m5/peak-motifs_oligos_7nt_vs_ctrl_m5.tab ; oligos_7nt_vs_ctrl_m5_tf /home/rsat/rsa-tools/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_7nt_vs_ctrl_m5/peak-motifs_oligos_7nt_vs_ctrl_m5.tf ; oligos_7nt_vs_ctrl_m5_vs_db_custom_motif_collection /home/rsat/rsa-tools/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_7nt_vs_ctrl_m5/peak-motifs_oligos_7nt_vs_ctrl_m5_vs_db_custom_motif_collection.tab ; oligos_7nt_vs_ctrl_m5_vs_db_custom_motif_collection_html /home/rsat/rsa-tools/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_7nt_vs_ctrl_m5/peak-motifs_oligos_7nt_vs_ctrl_m5_vs_db_custom_motif_collection.html ; oligos_7nt_vs_ctrl_m5_vs_db_jaspar_core_vertebrates /home/rsat/rsa-tools/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_7nt_vs_ctrl_m5/peak-motifs_oligos_7nt_vs_ctrl_m5_vs_db_jaspar_core_vertebrates.tab ; oligos_7nt_vs_ctrl_m5_vs_db_jaspar_core_vertebrates_html /home/rsat/rsa-tools/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_7nt_vs_ctrl_m5/peak-motifs_oligos_7nt_vs_ctrl_m5_vs_db_jaspar_core_vertebrates.html ; oligos_7nt_vs_ctrl_m5_vs_db_jaspar_pbm_mouse /home/rsat/rsa-tools/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_7nt_vs_ctrl_m5/peak-motifs_oligos_7nt_vs_ctrl_m5_vs_db_jaspar_pbm_mouse.tab ; oligos_7nt_vs_ctrl_m5_vs_db_jaspar_pbm_mouse_html /home/rsat/rsa-tools/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_7nt_vs_ctrl_m5/peak-motifs_oligos_7nt_vs_ctrl_m5_vs_db_jaspar_pbm_mouse.html ; oligos_7nt_vs_ctrl_m5_vs_ref /home/rsat/rsa-tools/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_7nt_vs_ctrl_m5/peak-motifs_oligos_7nt_vs_ctrl_m5_vs_ref.tab ; oligos_7nt_vs_ctrl_m5_vs_ref_html /home/rsat/rsa-tools/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/discovered_motifs/oligos_7nt_vs_ctrl_m5/peak-motifs_oligos_7nt_vs_ctrl_m5_vs_ref.html ; oligos_7nt_vs_ctrl_pssm_counts /home/rsat/rsa-tools/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/oligos_7nt_vs_ctrl/peak-motifs_oligos-2str-noov_7nt_vs_ctrl_pssm_count_matrices.txt ; oligos_7nt_vs_ctrl_pssm_logo1 /home/rsat/rsa-tools/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/oligos_7nt_vs_ctrl/peak-motifs_oligos-2str-noov_7nt_vs_ctrl_pssm_count_matrices_logo_m1.png ; oligos_7nt_vs_ctrl_pssm_logo2 /home/rsat/rsa-tools/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/oligos_7nt_vs_ctrl/peak-motifs_oligos-2str-noov_7nt_vs_ctrl_pssm_count_matrices_logo_m2.png ; oligos_7nt_vs_ctrl_pssm_logo3 /home/rsat/rsa-tools/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/oligos_7nt_vs_ctrl/peak-motifs_oligos-2str-noov_7nt_vs_ctrl_pssm_count_matrices_logo_m3.png ; oligos_7nt_vs_ctrl_pssm_logo4 /home/rsat/rsa-tools/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/oligos_7nt_vs_ctrl/peak-motifs_oligos-2str-noov_7nt_vs_ctrl_pssm_count_matrices_logo_m4.png ; oligos_7nt_vs_ctrl_pssm_logo5 /home/rsat/rsa-tools/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/oligos_7nt_vs_ctrl/peak-motifs_oligos-2str-noov_7nt_vs_ctrl_pssm_count_matrices_logo_m5.png ; oligos_7nt_vs_ctrl_pssm_logo_rc1 /home/rsat/rsa-tools/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/oligos_7nt_vs_ctrl/peak-motifs_oligos-2str-noov_7nt_vs_ctrl_pssm_count_matrices_logo_m1_rc.png ; oligos_7nt_vs_ctrl_pssm_logo_rc2 /home/rsat/rsa-tools/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/oligos_7nt_vs_ctrl/peak-motifs_oligos-2str-noov_7nt_vs_ctrl_pssm_count_matrices_logo_m2_rc.png ; oligos_7nt_vs_ctrl_pssm_logo_rc3 /home/rsat/rsa-tools/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/oligos_7nt_vs_ctrl/peak-motifs_oligos-2str-noov_7nt_vs_ctrl_pssm_count_matrices_logo_m3_rc.png ; oligos_7nt_vs_ctrl_pssm_logo_rc4 /home/rsat/rsa-tools/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/oligos_7nt_vs_ctrl/peak-motifs_oligos-2str-noov_7nt_vs_ctrl_pssm_count_matrices_logo_m4_rc.png ; oligos_7nt_vs_ctrl_pssm_logo_rc5 /home/rsat/rsa-tools/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/oligos_7nt_vs_ctrl/peak-motifs_oligos-2str-noov_7nt_vs_ctrl_pssm_count_matrices_logo_m5_rc.png ; oligos_7nt_vs_ctrl_pssm_sig /home/rsat/rsa-tools/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/oligos_7nt_vs_ctrl/peak-motifs_oligos-2str-noov_7nt_vs_ctrl_pssm_sig_matrices.tf ; oligos_7nt_vs_ctrl_pssm_tf /home/rsat/rsa-tools/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/results/oligos_7nt_vs_ctrl/peak-motifs_oligos-2str-noov_7nt_vs_ctrl_pssm_count_matrices.tf ; synthesis /home/rsat/rsa-tools/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/peak-motifs_synthesis.html ; test_converted /home/rsat/rsa-tools/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/data/sequences/peak-motifs_test.fasta ; test_purged /home/rsat/rsa-tools/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/data/sequences/peak-motifs_test_purged_ml30_mis0.fasta ; test_seq_coord /home/rsat/rsa-tools/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/data/sequences/peak-motifs_test_seqcoord.bed ; test_seqlen /home/rsat/rsa-tools/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/data/sequences/peak-motifs_test_seqlen.tab ; test_seqlen_distrib /home/rsat/rsa-tools/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/data/sequences/peak-motifs_test_seqlen_distrib.tab ; test_seqlen_distrib_graph /home/rsat/rsa-tools/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/data/sequences/peak-motifs_test_seqlen_distrib.png ; timelog /home/rsat/rsa-tools/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/reports/peak-motifs_timelog.txt ; timelog_html /home/rsat/rsa-tools/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/reports/peak-motifs_timelog.html ; timetable /home/rsat/rsa-tools/public_html/tmp/2012/07/02/peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/reports/peak-motifs_timetable.txt ; 2012-07-02.204115 (cd $RSAT/public_html/tmp/2012/07/02 ; zip -ryq peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg/peak-motifs_archive.zip peak-motifs.2012-07-02.203241_2012-07-02.203241_GH0tGg -x peak-motifs_archive.zip)