RNASeq
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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
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 |
