RNA-Seq analysis for differential expression

Trainer St├®phane Plaisance


You will

  • execute a complete analysis workflow at command line to detect differential expression between two conditions
  • initiate a functional annotation and interpretation of the differential expression results


  • We first perform quality control of the sequence reads to detect biases or leftover adaptors.
  • We then map the reads to the reference genome with use of a transcript database model.
  • We perform a detailed QC analysis of the mapping results to again detect potential problems.
  • The mapping data is adjusted to compensate for artifacts like duplicates.
  • The mappings are used to obtain transcript counts usable for differential expression.
  • The count tables are merged and used to compute differential expression using several programs.
  • We START a typical functional analysis of the obtained results similar to what is done for microarray data in order to exemplify handy tools and commercial alternatives.

The code pieces used during the training are made available through our Wiki as well as detailed results and can be copied and adapted for own user needs with minimal edits. Key results have been saved to our server and can be downloaded to fully reproduce the training.


Familiarity with

  • the Illumina sequencing process
  • basic NGS data formats: FASTQ, SAM/BAM, GTF, ...
  • the use of Linux command line

If you do not meet these requirements you have to follow the "Introduction to the analysis of NGS data" training.


See the TRAINING AT VIB website for a detailed schedule of this training.

Training material

All material is available on the wiki page


Scientific topics RNA-Seq, Differential expression analysis, Gene expression
Target audience Life Science Researchers, PhD students, post-docs, beginner bioinformaticians