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Old 05-10-2011, 09:06 PM   #1
ewilbanks
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Location: Davis, CA

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Question Single stranded coverage from sam/bam

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
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Old 05-11-2011, 07:43 AM   #2
adamdeluca
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genomeCoverageBed has a "-strand" flag
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Old 05-14-2011, 12:13 AM   #3
ewilbanks
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doh! missed that, thanks!!
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bam, coverage, coverage calculation, sam, strand-specific

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