SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
Minimum Read Length for BWA persorrels Bioinformatics 6 10-05-2013 11:03 AM
BWA - Why giving only one match per read ? Arupsss Bioinformatics 6 07-25-2012 09:41 AM
Problem with BWA mapping second read pbluescript Bioinformatics 3 10-12-2011 07:52 AM
BWA puzzle: Read fate is not deterministic? bhootnaath Bioinformatics 2 06-09-2011 11:50 AM
BWA Read Length AnamikaDarwin Bioinformatics 1 04-10-2009 11:47 PM

Reply
 
Thread Tools
Old 11-19-2013, 09:33 AM   #1
SFAB
Junior Member
 
Location: UK

Join Date: Aug 2012
Posts: 3
Default BWA XT:A:U and XA for same read?

Apologies if this has been asked before, but I can't see an answer and can't seem to figure this out.

Looking at the BWA documentation I see that XT:A:U denotes unique, while the XA tag gives alternative mappings. That makes me think I shouldn't get both XT:A:U (which I'm understanding to mean a read that maps uniquely) and XA, a read with more than one mapping for the same read. However, looking at a BAM file generated by BWA using samtools, that is what I'm seeing, both the XT tag with U and entries in XA for the same read.

If anyone could explain this, it would be appreciated.
SFAB is offline   Reply With Quote
Old 11-19-2013, 09:42 AM   #2
swbarnes2
Senior Member
 
Location: San Diego

Join Date: May 2008
Posts: 912
Default

Is this read paired end?

I think what might have happened is that the read by itself might be ambiguous, but maybe with the information from the mate pair, it can be properly placed, and maybe one tag wasn't changed to reflect that?

Or is it possible that it maps to the one location, but is only a single base off of the others?
swbarnes2 is offline   Reply With Quote
Reply

Tags
bwa, multiple alignments, tag, unique reads, xt:a:u

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 07:42 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2021, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO