Hg19 Strand Information Of Sam Output.

Question

[Coryza]

Hi all,

I've got Paired-End Illumina data mapped against the Human Hg19. When viewing the SAM output, how can I check if a pair mapped against the forward Hg19 genome sequence or against the reverse Hg19 genome sequence?

[Devon Ryan]

Is the data from a stranded/directional prep? If not, you can't. If so, which one, since this depends on that.

Edit: I should mention that I'm reading into your question that you want to know the original strand of the fragment sequenced by the paired-ends.

Edit2: And cross-posted at seqanswers.

Answer 1

[Sean Davis]

The information about strand of the read is in the FLAG column in the SAM file. You can use this little tool to look up the FLAG value to see what it represents:

http://picard.sourceforge.net/explain-flags.html

The SAM specification has more detail.