Hi, I am trying to look at differential binding of a number of chromatin regulatory proteins via CutandRun only at a predefined set of peaks (Approx. 5000 peaks).
When I carry out the analysis for different proteins at the same predefined peaks I get a different number of consensus peaks which is always less than 5000. I assumed the analysis would be carried out with the entire predefined peak-set as the consensus peaks and the number would stay the same. However, this does not seem to be the case. If you could provide some clarity on what is happening that would be much appreciated.
I am supplying my predefined peaks as a bed file at the sample file generation stage under the peaks column for each sample (3 replicates & 2 conditions)
Thank you in advance,