Hi, We are looking at the binding sites of TF that is not in the nucleus prior to its activation and one hour after giving a hormone treatment to the cells the TF is in the nucleus and can bind to DNA. We did ChIP-seq for both before and after the hormone treatment and our input is from the cells with the hormone. When I'm using MACS2 to call peaks I'm getting a lot more peaks in the non-treated cells (40000 compare to only 500 in the treated cells), which doesn't make any sense because the TF is not supposed to bind to DNA in the untreated cells. In addition, we know what is the motif of the factor and most of the peaks in the untreated cells don't have the motif (4%) while 70% of the 500 peaks from the treated cells do. My guess is that the peaks are some phantom peaks or noise, but why do I still detect them with MACS analysis and how can I remove these sort of peaks or "clean" my peaks so I can believe the peaks that I'm getting from the treated cells?
If you have any other suggestion to why I'm getting this odd results from the untreated cells I would also like to hear. I'll just mention that I have 15M reads in the treated cells and in the input and 8M reads in the untreated cells.