Selecting Opposite Orientation Strand Reads From .Sam File

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

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updated 13.3 years ago by Istvan Albert

• written 13.3 years ago by soosus •

duplicate of

samtools view: only forward or reverse strand

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written 13.3 years ago by Pierre Lindenbaum

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

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written 13.3 years ago by Pierre Lindenbaum

1 answer

See Explain SAM flags

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updated 6.6 years ago by Ram

• written 13.3 years ago by Istvan Albert

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