Are multi mapped reads used in ChIP-sea peaking calling such as MACS2?
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6 weeks ago
chao.xing ▴ 20

I wonder whether multi mapped reads are used in ChIP-sea peaking calling such as MACS2? If so, what are the suggestions on QC?

ChIP-seq peaking calling reads MACS2 multi-mapped • 273 views
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Yes, afaik only non-properly paired reads are removed. Hence, a MAPQ filter should be applied before peak calling, e.g. MAPQ > 10 or 20.

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If the multi-mapped reads are part of your BAM or BED file that you feed into MACS2, it will use them.

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