We are interesting in ChIP-seq small peak , we have avidence that the the small or weak peaks are functional sites , how to call weak peak using macs2？
I try to use the parameter q 0.05, but It can't call the weaker peaks.
There is no gold standard answer for this. You will need a good input control, probably chromatin input is the best sequenced to similar depths as the IP samples. You can use dedicated replicate-aware peak callers such as PePr or use other filtering strategies that increase confidence in your calls such as IDR or custom strategies like "peak has to be in at least 2/3 samples at FDR below a certain threshold". Still, confidence in small peaks requires excellent data quality. If you have a poor antibody then you will have a hard time calling weak binding events. Are you after a transcription factor? How is data quality?
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