Hi
I have a .BAM file which contains discordantly and concordantly mapped mate-pairs. I used bedtools Pairtobed to extract the mate-pairs which both show overlap with targeted regions (Illumina target .bed file). Is it somewhere possible to remove the parts of the mate-pairs that do not show overlap? I couldn't find it in the bedtools manual... can I just use intersectBed for each read for this?
Thanks!