February 4, 2022, 9:30 am
February 11, 2022, 4:30 pm


Bulk RNASeq: from counts to differential expression

The course consists of two separate sessions on the 4th and 11th of February, feautring a youtube session on counting and differential expression analysis in R and an online Q&A session to solve the exercises and answer all the questions that arise when trying the analysis on your own data.


The course will show:

  • Tools to generate count files like featureCounts, and htseq count are demonstrated
  • Count files from HTSeq-Count, FeatureCounts, Salmon or Kallisto are used to identify differentially expressed genes

After the live session participants can analyze their own count files. Issues can be handled during the Q&A session.

Software demonstrated

  • Counting using Galaxy: STAR, htseq-counts, FeatureCounts
  • Identification of DE using Bioconductor: DESeq2 + other packages like tximeta (script for EdgeR is provided but not demonstrated)
  • Visualization of results using R: ggplot2, pheatmap,
  • Mapping of IDs to Gene symbols using Bioconductor: AnnotationDbi 
Janick Mathys

VIB Bioinformatics Core training coordinator

Contact Janick Mathys : janick.mathys@vib.be