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Old 12-01-2011, 11:16 AM   #3
Location: Seattle

Join Date: Jul 2011
Posts: 98

Originally Posted by swbarnes2 View Post
Come on. If you aren't going to read the SAM format specs before you ask a question about the SAM format, at least search the message board before asking a question. I think I've answered this question three times this week alone.
Sorry. I had searched the message board unsuccessfully, but yes - it was stupid not to look at the sam documentation more closely:

4.1 For a unmapped paired-end or mate-pair read whose mate is mapped, the unmapped read should have RNAME and POS identical to its mate.

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