are there some tools or software can find the different peak of ATAC-seq

Question

[zhao03]

Hi i got the ATAC-seq peaks by MACS2 cellpeak, How can i find the different peak between case and cotrol? thank you!

Answer 1

[Rory Stark]

Another Bioconductor package, DiffBind, is often used to find differential ATAC peaks using a straightforward ChIP-seq workflow.

Answer 2

[eyleen.corrales]

You could take a look at this paper: https://epigeneticsandchromatin.biomedcentral.com/articles/10.1186/s13072-020-00342-y . They provide the scripts for doing what you want to do with csaw