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Hg19 Strand Information Of Sam Output.

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?

illumina paired-end hg19 sam
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updated by Biostar Biostar • written by Coryza • Coryza

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.

• 0 views • link
written by Devon Ryan Devon Ryan

1 answer

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.

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updated by Ram Ram • written by Sean Davis Sean Davis

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