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Introduction to RNASeq analysis


This course offers an introduction to RNASeq analysis. We will cover from raw reads to differential expression analysis.

Prerequisites

Linux for dummies

Program

  • Reads preprocessing
  • Mapping RNASeq reads against an annotated reference genome with STAR
  • Counting reads in transcrits/genes with HTSeq-count
  • Count normalization using Diane
  • Differential expression analysis using Diane
  • Plots, clustering, co-expression network: degust, WGCNA

Learning objectives

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

Training material

Instructors

  • Alexandre Sorianon (AS) - alexandre.soriano@cirad.fr
  • Catherine Breton (CB) - c.breton@cgiar.org
  • Gautier Sarah (GS) - gautier.sarah@cirad.fr
  • Julie Orjuela (JO) - julie.orjuela@ird.fr
  • Aurore Comte (AC) - aurore.compte@ird.fr
  • 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
2022 Montpellier, France Introduction to transcriptomics analysis 10 CB, GS, AS   UMR DIADE, AGAP, MIVEGEC, PHIM
2019 Montpellier, France Introduction to transcriptomics analysis 20 JO, CB, GS, SC, AC   UMR DIADE, IPME, AGAP, Bioversity
2018 Montpellier, France Introduction to transcriptomics analysis 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