I have a set of .BAM files (with reads) on different histone marks but I do not have replicates.
The files that I have are H3K27ac (untreated), H3K27ac (treated with sample1) and H3K27ac (treated with sample2).
I have already called peaks on these samples using MACS2.
I want to identify differential peaks across these three.
a) How can I identify these peaks?
b) Is their any package available to do so, if yes, have you used it?