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