RNAseq alignment, quantification and transcript discovery with Galaxy (25/08/2016)

This training session, organized jointly with the Sigenae platform, is designed to help you deal with sequences from the SGS (Second Generation Sequencing) particularly Illumina platforms (HiSeq). You will discover the new sequence file formats, learn about the usual biases of this data type and run different kind of analysis such as spliced alignment on a reference genome, novel gene and transcript discovery, expression quantification of the genes and transcripts.



This training focuses on practice. It consists of four modules with a large variety of exercises described hereunder:

  • Introduction (09:00 am to 10:30 am): what is gene expression? What kind of technology can be used to monitor gene expression? What do the reads produced by SGS platforms (Illumina) using the RNA-Seq protocol look like? Which are the known biases of these sequences?
  • Splice aligning reads on a reference genome (10:45 am to 12:30 pm).
  • Visualizing alignments and splice sites using IGV (Integrated Genome Viewer) (14:00 pm to 15:30 pm).
  • Discovering novel genes and transcripts, Quantifying gene and transcript expression (15:45 pm to 17:00 pm).


The session will take place in the formation room of the INRA center of Toulouse-Auzeville.


Prerequisites: ability to use a Galaxy environment (see “Galaxy : First steps” training). Training materials (Slides, exercises and corrections) will be given to you during the session.



Bookings: RNAseq alignment, quantification and transcript discovery with Galaxy

Bookings have closed for this event.