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RNASeq analyses (using Galaxy and TOGGLe)


This course offers an introduction to RNASeq analyses using two different workflow management systems: Galaxy and TOGGLe. This includes reference-based mapping, estimates of transcript levels, differential expression (DE) analyses, visualization of statistics results.

Prerequisites

Workflow management system (Galaxy, TOGGLe)

Program

  • Pseudo-mapping RNASeq reads against a reference transcriptome by using with kallisto (Galaxy)
  • Mapping RNASeq reads against an annotated reference genome with Hisat2 (TOGGLe)
  • Counting reads in transcrits/genes with Stringtie (TOGGLe)
  • Differential expression analysis using EdgeR and DESeq2 (Pivot and R)
  • Plots, clustering, co-expression network: degust, WGCNA (R and Galaxy)

Learning objectives

  • Manipulate packages/tools available for searching DE genes
  • Think about different normalisation methods
  • Detect differentially expressed genes
  • Compare results between approaches

Training material

Instructors

  • Julie Orjuela (JO) - julie.orjuela@ird.fr
  • Aurore Comte (AC) - aurore.compte@ird.fr
  • Gautier Sarah (GS) - gautier.sarah@cirad.fr
  • Catherine Bréton (CB) - c.breton@cgiar.org
  • Christine Tranchant (CT) - christine.tranchant@ird.fr
  • Sebastien Ravel (SR) - sebastien.ravel@cirad.fr
  • Alexis Dereeper (AD) - alexis.dereeper@ird.fr
  • Sebastien Cunnac (SC) - sebastien.cunnac@ird.fr

Trainings

Date Location Topics Parrticipants Instructors Links Units
2019 Montpellier, France Introduction to transcriptomics analyses 20 JO, CB, GS, SC, AC   UMR DIADE, IPME, AGAP, Bioversity
2018 Montpellier, France Introduction to transcriptomics analyses 20 CT, SR, AD, SC   UMR DIADE, IPME, BGPI
2016 Ouagadougou, Burkina Bioinformatics applied to genomics 20 CT, AD   IRD
2015 Hanoi, Vietnam Bioinformatics applied to genomics 20 AD   LMI Rice
2014 Dakar, Senegal Bioinformatics applied to genomics 20 CT, AD   IRD, Bel Air Campus