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Introduction to RNASeq analysis in Galaxy

In the context of a collaboration between IRD and Universidad Nacional de Colombia in Bogota,
a training session is organized to give an introduction to RNASeq analysis in the Galaxy environment.
We will cover from raw reads to differential expression analysis.

With the support of:
Coordinación Curricular del Postgrado Biologia Centro de Excelencia en Computación Científica.


Genomics knowledge


  • Introduction to Galaxy
  • Discovering Galaxy functionalities
  • Reads preprocessing
  • Mapping RNASeq reads against an annotated reference genome with STAR
  • Counting reads in transcrits/genes with HTSeq-count
  • Count normalization using DESeq2
  • Differential expression analysis using DESeq2
  • Plots, clustering

Learning objectives

  • Familiarize with Galaxy environment
  • Process raw reads to count matrix
  • Think about different normalisation methods
  • Detect differentially expressed genes
  • Compare results between approaches

Training material

  • Galaxy introduction (Slides) : see
  • Galaxy first Practice : see
  • Introduction to RNASeq (Slides): see
  • RNASeq analysis (Practice) : see


  • Alexis Dereeper (AD) -
  • Camilo Ernesto Lopez (Universidad Nacional de Colombia (UNAL)) -
  • Clara Isabel Bermudez Sanata (Universidad Nacional de Colombia (UNAL)) -