Hi all! I have (probably very naive) questions regarding the choice of peaks that were generated by MACS2. I have done chip-seq on a chromatin binding protein (not TF) using arabidopsis tissues . After analysis, MACS2 gives me approximately 2200 peaks which I later annotated. At this point, I am not quite sure what to do next. If anybody could help me, I would greatly appreciate it. 1. Does every peak represent a real binding site? Is the summit the binding site? 2. If only select peaks represent binding sites, how could I filter these peaks to get only the true binding sites? Should I use the score, signal value, p-value or q-value to do so?
Thank you for any help!!!!