RNASeq analyses (using Galaxy and TOGGLe)
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Description
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
Mapping of RNASeq against a transcriptome reference with kallisto (Galaxy)
Mapping of RNASeq against an annotated genome reference with TopHat (TOGGLe)
Differential expression analysis using EdgeR and DESeq2
Plots, clustering, co-expression network: degust, WGCNA


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


Instructors
Alexis DereeperĀ - alexis.dereeper@ird.fr
Sebastien Cunnac - sebastien.cunnac@ird.fr
Sebastien RavelĀ - sebastien.ravel@cirad.fr
Christine TranchantĀ  - christine.tranchant@ird.fr