how to extract the sense and antisene bam files from the single end mapping bam file?

Question

[wu.zhiqiang.1020]

Dear all,

I have one bam file produced from single end RNAseq reads using Gsnap. I want to extract the separated bam files for sense and antisense reads only.

I know that the samtools could use to extract them by flag for pair ens read bam file. But what's the flag number for single end reads bam file? what's the commands for single end bam file?

Or what other tools could be used to extract the sense and antisense reads bam file from one total bam file?

Thanks!

ZQ

Answer 1

[Pierre Lindenbaum]

It's the same flag: use -f 16 or -F 16 to include/exclude the reads on the reverse strand

[michael.ante]

If you want to split the file according to the strand, you should follow Pierre's answer.

If you want to have the sense/antisense reads according to the transcripts' orientation, you should use for instance intersectBed with the -s and -S options.

[wu.zhiqiang.1020]

Thanks. I will do your suggestion to try. if I have problem, I will post here. Cheers!