What it does

Performs digital differential gene expression analysis between two groups (eg a treatment and control) each with biological replicates, from count data arranged in a matrix as a tabular file.

Input

A matrix consisting of non-negative integers. The matrix must have a unique header row identifiying the samples, as well as a unique set of row names as the first column. To create appropriate input files, the "Multiple BAMs to matrix" tool takes multiple bam files containing mapped RNAseq reads mapped to a reference genome, and a BED file containing (eg Refseq) contigs. A count matrix containing contigs as rows and samples as columns will be created and can then be used in this tool to estimate differential gene expression using methods appropriate for count data.

Output

A tabular file containing relative expression levels, statistical estimates of differential expression probability, the R script, log and sessionInfo, and some helpful diagnostic plots.

Attribution DGE.R was originally written by: S.Lunke and A.Kaspi. Wrapping for Galaxy and general kibbitzing from Ross Lazarus. This tool wrapts the edgeR Bioconductor package so all calculations and plots are controlled by that code. See edgeR for all documentation and appropriate attribution. Recommended reference is Mark D. Robinson, Davis J. McCarthy, Gordon K. Smyth, PMCID: PMC2796818