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Feature request: paired-end stranded RNA-seq .bam #140

Open GoogleCodeExporter opened 9 years ago

GoogleCodeExporter commented 9 years ago 
We are using coverageBed and genomeCoverageBed to calculate signal on annotated 
exons and whole genome for stranded paired-end RNA-seq data. 

The standard SAM/BAM convention is to assign strands to the mates that agree 
with the actual sequences. In our protocol this leads to the 1st mate being on 
opposite strand to the RNA sequence, and the 2nd mate on the same strand as RNA.

To generate correct signal with bedTools commands, we need to generate a new 
.bam file converting the strands of the mates so that they agree with the RNA 
strand. It would be great if this conversion was implemented as a bedTools 
flag, like -sr1 for reverting strand of mate 1 and -sr2 for reverting strand of 
mate 2.

Original issue reported on code.google.com by adobin@gmail.com on 13 Sep 2012 at 8:46