compare-matrices -v 1 -mode matches -format1 transfac -file1 Myogenin_Rep3_motifs50/results/discovered_motifs/dyads_m24/peak-motifs_dyads_m24.tf -format2 tf -file2 $RSAT/public_html/motif_databases/JASPAR/Jaspar_2020/nonredundant/JASPAR2020_CORE_vertebrates_non-redundant_pfms.tf -mode matches -strand DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.7 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,width,strand,offset,alignments_1ton -sort Ncor -quick -o Myogenin_Rep3_motifs50/results/discovered_motifs/dyads_m24/peak-motifs_dyads_m24_vs_db_jaspar_core_nonredundant_vertebrates Program version 1.118 Quick mode Input files file2 $RSAT/public_html/motif_databases/JASPAR/Jaspar_2020/nonredundant/JASPAR2020_CORE_vertebrates_non-redundant_pfms.tf file1 Myogenin_Rep3_motifs50/results/discovered_motifs/dyads_m24/peak-motifs_dyads_m24.tf Output files alignments_1ton Myogenin_Rep3_motifs50/results/discovered_motifs/dyads_m24/peak-motifs_dyads_m24_vs_db_jaspar_core_nonredundant_vertebrates_alignments_1ton.tab match_table_txt Myogenin_Rep3_motifs50/results/discovered_motifs/dyads_m24/peak-motifs_dyads_m24_vs_db_jaspar_core_nonredundant_vertebrates.tab html_index Myogenin_Rep3_motifs50/results/discovered_motifs/dyads_m24/peak-motifs_dyads_m24_vs_db_jaspar_core_nonredundant_vertebrates_index.html alignments_1ton_html Myogenin_Rep3_motifs50/results/discovered_motifs/dyads_m24/peak-motifs_dyads_m24_vs_db_jaspar_core_nonredundant_vertebrates_alignments_1ton.html match_table_html Myogenin_Rep3_motifs50/results/discovered_motifs/dyads_m24/peak-motifs_dyads_m24_vs_db_jaspar_core_nonredundant_vertebrates.html prefix Myogenin_Rep3_motifs50/results/discovered_motifs/dyads_m24/peak-motifs_dyads_m24_vs_db_jaspar_core_nonredundant_vertebrates Matrices file1 1 matrices Myogenin_Rep3_motifs50/results/discovered_motifs/dyads_m24/peak-motifs_dyads_m24.tf file1 1 18 34 file2 746 matrices $RSAT/public_html/motif_databases/JASPAR/Jaspar_2020/nonredundant/JASPAR2020_CORE_vertebrates_non-redundant_pfms.tf file2 1 6 24 file2 2 17 100 file2 3 10 9897 file2 4 17 101 file2 5 17 3851 file2 6 10 25318 file2 7 6 27 file2 8 11 1001 file2 9 14 101 file2 10 6 20 file2 11 8 104 ... 736 more matrices Column content 1 id1 Identifier of the first matrix 2 id2 Identifier of the second matrix 3 name1 Name of the first matrix 4 name2 Name of the second matrix 5 cor Pearson coefficient of correlation between frequency matrices 6 Ncor Normalized correlation. Ncor = cor * Wr 7 w1 Width of the first matrix 8 w2 Width of the second matrix 9 w Alignment length (number of overlapping columns between matrix 1 and matrix 2, as a function of the offset) 10 W Total alignment length (overlapping + non-overlapping columns). W = w1 + w2 - w 11 Wr Relative alignment length (overlap divided by the total alignemnt length). Wr = w/W 12 wr1 Alignment length relative to the width of the first matrix. wr1 = w/w1 13 wr2 Alignment length relative to the width of the second matrix. wr2 = w/w2 14 strand "strand", i.e. orientation of matrix 2 relative to matrix 1 (D=direct; R=reverse) 15 offset shift of the second matrix relative to the first matrix (negative:left; positive: right)
| id1 | id2 | name1 | name2 | cor | Ncor | w1 | w2 | w | W | Wr | wr1 | wr2 | strand | offset |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| dyads_m24 | MA1118.1 | dyads_m24dyads_m24 | SIX1 | 0.722 | 0.441 | 18 | 11 | 11 | 18 | 0.6111 | 0.6111 | 1.0000 | D | 3 |
| dyads_m24 | MA0606.1 | dyads_m24dyads_m24 | NFAT5 | 0.737 | 0.409 | 18 | 10 | 10 | 18 | 0.5556 | 0.5556 | 1.0000 | R | 7 |
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