Entering edit mode
6.0 years ago
yp19
▴
70
I have paired end data in a SAM file and I want to extract all the reads which correspond to specific contig ids. My contig ids are in a text file with one ID per line.
Output of SAM/BAM is preferred.
Thanks for your help.
many duplicates. e.g: Extract ONLY chromosomes 1-22 from bam file - removing extraneous chr annotations ...
would the solution in that link also work for paired data? Thanks!
@max_19 why wouldn't it work for paired data ?
If one read in a pair matches the contig but the other read in that pair does not. Is there a way to include that pair even if only one read matches?