BioC2014: RNA-Seq workflow for differential gene expression

This lab will walk you through an end-to-end RNA-Seq differential expression workflow. We will start from the FASTQ files, align to the reference genome, prepare gene expression values as a count table by counting the sequenced fragments, perform differential gene expression analysis, and visually explore the results. This lab covers the basic introduction. For a more in-depth explanation of the advanced details, we advise you to proceed to the vignette of the DESeq2, Differential analysis of count data – the DESeq2 package. For a treatment of exon-level differential expression, we refer to the vignette of the DEXSeq package, Analyzing RNA-seq data for differential exon usage with the DEXSeq package