Question

Selecting Opposite Orientation Strand Reads From .Sam File

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11.0 years ago

soosus ▴ 90

I'd like to construct a simple, single-line bash (or bash/perl) command to return all reads from a .SAM file that mapped in opposite orientation to the reference (-). I'm shaky on how to derive this information from a .SAM file. Suggestions?

sam strand bash • 3.4k views

ADD COMMENT • link updated 11.0 years ago by Istvan Albert 100k • written 11.0 years ago by soosus ▴ 90

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duplicate of

samtools view: only forward or reverse strand

ADD REPLY • link 11.0 years ago by Pierre Lindenbaum 161k

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this post was deleted. Please, keep it for reference. Thxs.

ADD REPLY • link 11.0 years ago by Pierre Lindenbaum 161k

Ram · Answer 1 · 2013-04-30

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11.0 years ago

Istvan Albert 100k

See Explain SAM flags

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ADD COMMENT • link updated 4.4 years ago by Ram 43k • written 11.0 years ago by Istvan Albert 100k