I have a group of specific H3K27ac ChIP-seq peaks. I want to generate corresponding random control regions and then do some comparison. It seems that bedtools shuffle is a general way to do this. But I think the decent random control should be located in regions with relatively high nucleosome occupancy. I happened to have a very high-resolution H3 ChIP-seq data(enough to detect 1bp nucleosome phasing...). The problem is that I do not know how to get the "H3-depleted" regions (used as mask regions in bedtools shuffle). Calling peaks is not an option (H3 ChIP is flat)
Is it the right way to do this? Could you please give me some guidance?