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Old 07-29-2014, 11:06 PM   #2
davetang
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Location: Japan

Join Date: Jul 2010
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I have exactly the same question and I haven't been able to find more detailed information on the XT:A:M tag from BWA.

I created a simple example (on my blog at http://davetang.org/muse/2014/07/24/...red-end-reads/; specifically the "RESCUING AMBIGUOUSLY MAPPED READS" section) trying to obtain the XT:A:M tag by aligning a uniquely- and multi-mapping pair but I got the XT:A:U and XT:A:R tags instead.

Last edited by davetang; 09-09-2014 at 03:41 AM. Reason: Removed the semi-colon from the URL.
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