SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
BWA - number of sequences aligned Cbon Bioinformatics 7 05-13-2012 03:45 PM
Are these reads aligned to my reference (BWA)? phatjoe Bioinformatics 2 03-01-2012 04:13 PM
BWA Reports High Mapping Quality for Poorly Mapped Pairs mdjones66 Bioinformatics 1 01-16-2012 08:29 PM
Current read1, index, and read2 primers for HiSeq2000 SeqVicious Illumina/Solexa 1 09-26-2011 02:12 PM
pick out nonmapped pairs from bwa louis7781x Bioinformatics 7 07-23-2011 10:39 PM

Reply
 
Thread Tools
Old 03-16-2012, 01:38 PM   #1
jflowers
Member
 
Location: New York, NY

Join Date: Oct 2011
Posts: 41
Default BWA aligned pairs read1=XT:A:U, read2=XT:A:R

Hello,

I've aligned Illumina paired end reads with BWA, filtered using samtools view -f 3 -F 12 ("proper pairs", both mates mapped).

I'm looking at the XT tags and see expected classes, where both mates are XT:A:U (both "unique") and XT:A:M + XT:A:U (one mate-rescued, one "unique").

However, I also find a class of paired reads where one read is XT:A:R (multiply-mapped) and the other is XT:A:U. This class of reads is a significant fraction of the total pairs (~10%) and the class persists after filtering on MAPQ > 20.

I anticipated that this class of reads would instead be classifed in the XT:A:M + XT:A:U (ie XT:A:R converted to XT:A:M), but apparently not.

Are the XT:A:R whose mate is XT:A:U mate-rescued, or something else?

Thanks.
jflowers is offline   Reply With Quote
Old 07-29-2014, 10:06 PM   #2
davetang
Member
 
Location: Japan

Join Date: Jul 2010
Posts: 11
Default

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 02:41 AM. Reason: Removed the semi-colon from the URL.
davetang is offline   Reply With Quote
Reply

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 12:46 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2019, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO