Selecting Opposite Orientation Strand Reads From .Sam File

Question

[soosus]

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?

[Pierre Lindenbaum]

duplicate of

samtools view: only forward or reverse strand

[Pierre Lindenbaum]

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

Answer 1

[Istvan Albert]

See Explain SAM flags

and other biostar posts:

• samtools view: only forward or reverse strand
• flag in sam format
• How to interpret the flag field in the SAM specification

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