SEQanswers - View Single Post - BWA aligned pairs read1=XT:A:U, read2=XT:A:R

davetang · 07-29-2014, 11:06 PM

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.

07-29-2014, 11:06 PM	#2
davetang Member Location: Japan Join Date: Jul 2010 Posts: 11	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.