The question is related to ChIP-seq, whether we should (at least in my case), consider a genomic loci with high IP signal over background even though there is no peak identified?
Following is the situation in one of my ChIP-seq analyses, in following figure, panel A, I found peaks (co-bound) for proteins (
P1, P2, P3) before and after treatment. There is another class of peak set, panel B, which were identified to be only bound by
P3. But as you can see, for
P2, we still have good amount of signal at these regions. Y-axis is log2 ratio of IP over background.
It is difficult to explain, example for P2, at a log2 ratio value of
1 or 1.5 there is a peak in panel A, but not in panel B. But the biological evidence is almost always
P3 is co-bound with
P2. I was just wondering if I just proceed with the analysis with the current peak set, I would miss a lot of important genes. On the other hand, there is no (to my knowledge) best way to address this issue.
At this point, I am considering to
- Calculate the average fold change (or log2 ratio compared to background) at which a real peak is identified for proteins
- If peak sets from panel B show fold change/log2 ratio for protein
P2above the fold change identified from step 1, I will merge them to panel A.
MACS2 to identify peaks with genomic background and
bamCompare for calculating log2 ratios over background
Any suggestions or ideas would be greatly appreciated.