Help to get differential_peaks.bed to use for findMotifsGenome.pl?
Hi all,
I am trying to use the command findMotifsGenome.pl from HOMER that needs differential_peaks.bed file as input. I used nf-core/atac-seq then DiffBind but not sure how to get differential_peaks.bed file. Would you please have a suggestion? Do I need to use DeSeq2 in this case? Also would you please tell me how to get background_peaks.bed file? Thanks a lot!
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