|
Introduction to RNASeq analysisThis 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
Instructors
- Guilhem Sempéré (GS) - guilhem.sempere@cirad.fr
- 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 |
| 2023 | Montpellier, France | Introduction to transcriptomics analysis | 15 | CB, GS, AS, GS | Bioversity , AGAP, AGAP | |
| 2022 | Montpellier, France | Introduction to transcriptomics analysis | 10 | CB, GS, AS | Bioversity , AGAP , AGAP | |
| 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 |