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modify the flag field in SAM
Hi,
I have PE data in a sam file. I would like to reverse complement all the reads. +- pairs becomes -+, -- becomes ++ ... but query sequence field can remain unchanged.
For eg, a read with flag 34 must become 18: the read is still in a proper pair, but maps on the opposite strand (all other bits must remain unchanged).
I can't figure out how to do this rapidely.
Thank you very much for your help
I have PE data in a sam file. I would like to reverse complement all the reads. +- pairs becomes -+, -- becomes ++ ... but query sequence field can remain unchanged.
For eg, a read with flag 34 must become 18: the read is still in a proper pair, but maps on the opposite strand (all other bits must remain unchanged).
I can't figure out how to do this rapidely.
Thank you very much for your help