I am analyzing H3K27Ac ChIP seq samples from paired samples from disease and healthy tissues (each pair from one individual).
Peaks were called with MACS2. The number of peaks and the FRiP (fraction of peaks in reads) is very different between the two experimental groups: IPsample NumberPeaks FRiP Disease1 73186 11 Disease2 56963 6.3 Disease3 106123 18 Disease4 58564 8.3 Normal1 18400 2 Normal2 25585 2.9 Normal3 37038 3.6 Normal4 24459 2.8
I don't know whether the difference is due to real biology, or due to some technical problem. I used DiffBind for detecting differential H3K27Ac. As expected I get much more peaks which are up at the disease tissue. Are there any suggestions for what would be the best normalization in DiffBind in such a case, or how can I try understanding whether this is an artifact? Thank you