Help with Diffbind and multiple conditions


I am trying to use Diffbind to analyze by ChIP-Seq data. I am looking at one epigenetic mark, and have five different conditions (Control treatment, Drug 1, Drug 2, Drug 3, Drug 4) with 2 replicates per condition. I uploaded .bam files and .narrowpeak files for each of the conditions and replicates and did this by adding 5 groups (using the “+Insert Group” button) in the Galaxy instance of Diffbind. Diffbind ran fine, but in my output it looks like only 2 of the groups (Control treatment vs Drug 1) were analysed. I am not sure why the remaining groups were not analysed. I am wondering if I am doing something wrong, and would be grateful for some help in ensuring that all five conditions are analysed.

Thank you!

Welcome, @os306

Diffbind wrapped in Galaxy computes one pairwise comparison per run.

The primary emphasis of DiffBind is on identifying sites that are differentially bound between two sample groups.