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reskejak / ATAC-seq

Basic workflow for ATAC-seq analysis
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ChIP-seq broadpeaks analysis #19

Open allaway opened 2 weeks ago

allaway commented 2 weeks ago

Hi there, this is a bit of a shot in the dark, but I'm trying to wrap my head around analyzing broadPeak chip-seq files and stumbled across this repo. The approach described in https://github.com/reskejak/ATAC-seq/blob/master/csaw_workflow.R seems like it could also work nicely for MACS2 broadPeak files from processing ChIP-seq data.

I was just curious if you had any thoughts - can this R script be repurposed for ChIP-seq/are there any gotchas that you recommend I look out for? Thank you!

reskejak commented 4 days ago

Hi,

Yes - I have used this workflow frequently for MNase-ChIP-seq data with PE data using calling and testing broadPeaks, for chromatin marks or regulators that operate on nucleosomes. Obviously, you would not perform the Tn5 coordinate shifting, but otherwise the workflows are nearly identical. Also, note that MACS2/3 have some newer features that reduce the need for constructing the BEDPE file (you can just supply PE BAM files now).

You can check out this relatively recent publication for examples of such applications in ChIP-seq: https://bmcbiol.biomedcentral.com/articles/10.1186/s12915-022-01407-y