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?