Entering edit mode
4.0 years ago
huangweiping.official
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10
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 asIDR
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?