My team has completed the steps till MACS2 using BED files for diseased and control datasets but we need the parameters for the Diffbind step to do differential analysis.
diffbind has not many parameters, the important step is that you “design” your diffbind experiment well. Meaning setting the groups correctly and providing the correct files.
Hope that helps,
Hey thanks for your reply l have another doubt What are the parameters for doing edgeR for analysing ATAC seq.