I'm trying to find a way to split reads mapped with STAR into two separate bam-files, one for each strand. STAR is able to do that when creating bedgraph or bigwig outputs (--outWigType and --outWigStrand), however I can not find any option to split raw reads into two separate files correponding to the strand they were transcribed from. I do not want to get counts per gene, I know how to do that, instead I need to get actual reads for each strand. Any ideas?
Thanks a lot in advance