South Green Trainings pages

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.

Prerequisites

Genomics knowledge

Program

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

Instructors

Alexis Dereeper (AD) - alexis.dereeper@ird.fr
Camilo Ernesto Lopez (Universidad Nacional de Colombia (UNAL)) - celopezc@unal.edu.co
Clara Isabel Bermudez Sanata (Universidad Nacional de Colombia (UNAL)) - cibermudezs@unal.edu.co