How to remove Mate mapped to a different chromosome

Question

[rohitsatyam102]

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?

Answer 1

[ATpoint]

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.

[kalavattam]

This post does not address their removal from a bam file; instead, it addresses their extraction to a new file.