I am interested to know if the differential binding analysis across different biological conditions makes sense or not. For example, if there are 2 different samples say A and B, where A is IPed using antibody P1 and B is IPed using antibody P2. and have their respective inputs. One does the peak calling using the inputs and get the set of peak for both the samples. Now, you find that a peak at certain genomic loci is present in both A and B; however, looking at the IGV plot you find that the peak in A has more reads than peak in B (considering that all the samples are normalized). When you do the differential analysis you find that the enrichment of the peak is significant in A more than B. Based on the above scenario, I have few questions:
1) I would like to know if such differential analysis makes sense or not ? 2) How can a peak be quantified same as the peak in RNA-Seq ? In RNA-Seq, you quantify the peaks because biologically, one knows there be can multiple copies of same mRNA
Ideally, I think a peak that is present should be considered as 1 and 0 if not. Please correct me if I wrong.