Single stranded coverage from sam/bam

[ewilbanks]

Hi all,

Does anyone know of a fast, handy way to calculate coverage of the forward and reverse strands in a genome independently?

I have a (really hacky) script that works on my data but was hoping someone has a more elegant solution. At the moment, I've been sorting my sam file into a fwd.reads.sam and rev.reads.sam, converting to bam files and then using Aaron Quinlan's bedTools (which is fantastic), like so...

genomeCoverageBed -d -ibam FWD.READS.EXAMPLE.bam -g MY_genome_file.txt > SINGLE_STRAND_COVERAGE.tsv`;

Any hope there's a way to do this single strand coverage calculation directly on the bam files and avoid all the icky sorting I've been doing?

Thanks!!!
Lizzy

[adamdeluca]

genomeCoverageBed has a "-strand" flag

[ewilbanks]

doh! missed that, thanks!!