Different parameters for macs2 to call narrow marks and broad marks?
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2.1 years ago
ben.kunfang ▴ 30


I was wondering how to set different parameters for macs2 to call different histone marks? I have seven marks: H3K4me1, H3K4me3, H3K27ac, H3K36me3, H3K79me2 H3K27me3 and H3K9me3. In my knowledge, H3K4me3 and H3K27ac should be narrow peak, H3K36me3, H3K27me3 and H3K9me3 should be broad peak. H3K4me1 is mix of localized and dispersed peak. Not sure for H3K79me2 but I guess it is also broad peak?

In this cases, should I use --call-summit for narrow marks and --broad for broad marks? Or just set a higher p value or q value for broad marks? And what should I do for H3K4me1? Any suggestions and advice are appreciated!

Thanks in advance! Kun

ChIP-Seq macs2 histone modification peak • 1.1k views

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