Peak calling for CUT&Tag data
Hi
I'm working with CUT&Tag data and have used MACS2 and SEACR to call peak for two biological replicates. The number of peak called by SEACR is much higer than the number of peaks called by MACS2. However, the percentage of overlapped peak of two replicates called from SEACR is less than 50%.
Is there any peak calling software perform better for CUT&Tag data?
Thank you very much in advance.
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SEACR was specifically developed for CUT&RUN, so this should be your go-to. If you have disagreement between replicates I would rather try and figure out why that is rather than questioning the peak caller. Is it a data-quality problem, so one good and one bad replicate?