Hi all!
When I generated the alignment statistics using Samtools Flagstat, I came across "mate mapped to a different chr". I was advised to remove these reads by my senior because then such reads will might introduce ambiguity at the time of peak calling. I checked out the various posts that underline the usefulness of this step on Biostars. However, none of them mention how to remove them.
Can someone help?
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rohitsatyam102
Extracting Paired-End Reads Sitting In Different Chromosomes
Peak calling by macs won't /should not be affected because macs only counts properly-paired reads which these aren't.
This post does not address their removal from a bam file; instead, it addresses their extraction to a new file.
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