I am working on a chip-seq data of general H3 histone antibody. As expected, there is not much difference between treatment group and control group, and I got so few peaks using MACS2 that I can hardly proceed further annotation and GO analysis.
I know it`s kind of weird to use such an antibody, but I am trying to find whether there are still H3 in the nucleus in my mutant.
In this case, what kind of peakcaller would be the best to use? I tried MACS2 and SICER2, but they both output poor number of peaks(less than 500). I assume that if there really are peaks of H3 they should be broad, but adjusting parameters to broad mode in MACS2 would not work.