Teachers

Schedule

Day Session Contents
Mon 23 Jan 10:00-11:00 Welcome to the course
Intro to high-throughput sequencing
11:30 - 14:00 First connection to Galaxy + registering
ChIP-seq: Read mapping
Chip-Seq
Tue 24 Jan Chip-Seq
Wed 25 Jan RNA-seq
Thu 26 Jan RNA-seq
Fri 27 Jan Analysis of personal projects
First contact with R (optional)

Course material

Slides

Teachers Topics Files
JvH Introduction to the course [pdf]
DP High-throughput sequencing technologies [pdf]
ChIP-seq
DP + JvH + CR (minimal) Introduction to ChIP-seq technology and applications [pdf]
DP + JvH + CR Read mapping for ChIP-seq [pdf]
DP + JvH + CR ChIP-seq analysis with Galaxy [pdf]
JvH From peaks to motifs [pdf]
RNA-seq
DP + JvH + CR RNA-seq analysis with Galaxy [pdf]

Board pictures

All participants are welcome to drop their pictures of the white board (or any other relevant material to add to the course) via a google drive link (with invitation).

The white board pictures are available here:

White board pictures

Web resources for the course

Resource Description + URL To install locally
TIB 2017 homepage http://congresos.nnb.unam.mx/
TIB 2017 Galaxy http://congresos.nnb.unam.mx/TIB2017/galaxy/
Galaxy server Galaxy server for the TIB2017 training http://132.248.220.36/
IGV Integrative Genomics Viewer http://software.broadinstitute.org/software/igv/ X
R R statistical package https://www.r-project.org/ X
RStudio An environment to manage R programming and projects https://www.rstudio.com/ X
GEO Gene Expression Omnibus https://www.ncbi.nlm.nih.gov/geo/
ArrayExpress Gene expression database https://www.ebi.ac.uk/arrayexpress/
RSAT Regulatory Sequence Analysis Tools http://rsat.eu/

Going further

How to use Galaxy beyond this training workshop?

Many solution exist.

  1. Main public server maintained by the Galaxy project: https://usegalaxy.org/
  2. National / regional / local shared facilities.
  3. Install a server in your institute.
  4. Install a server on your own machine.

How to get more advanced galaxy training?

Galaxy is a very active community which, from the very beginning of the project, devoted time to develop training supports.

  1. Within yur Galaxy connection, browse the Help menu: links to

  2. Learn galaxy wiki: https://wiki.galaxyproject.org/Learn

Courses on variant calling

  • Ecole de Bioinformatique Aviesan/IFB: