Downstream of Csaw differential binding region

Question

[Jingyue]

Dear all, I have a question of downstream analysis after I got the differential binding (DB) region from Csaw tool, which used a window-based method. My questions are:

• Since it is not a peak involved method, do I overlap these DB region (window-clustered region) back to my MACS2 peaks?
• If I would like to know how protein-A peaks falls in to protein-B DB regions in WT compare to protein-A knockdown, can I directly overlap peaks to DB region? or you would recommend me to overlap peaks to peaks?

Thank you for your suggestions!