how can chip seq macs2 call peaks filter Pvalue
hello everyone,I am using macs2 call my chip seq TF data.Now I have some confused about the peaks .I got the peaks bed file,I loaded the file and corresponding bw files(using deeptools produce the bw files from bam files ) in IGV,I found that some peaks that their Pvalues(-log10 Pvalue) were little ,like 9.7 were false peaks,but the peaks pvalue is very large like 54 is very true .Now my question is that I filter the Pvalue (by threshold value like 20 or 30 ) is reasonable? Thank you
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The answer depends a bit on what you're going to do with the resulting list. But generally there is nothing wrong in setting more stringent filters. I also suggest you take the FDR/adjusted p-value into consideration.
thank you ,I try it .