SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics

Similar Threads
Thread Thread Starter Forum Replies Last Post
Question on mapping quality and uniquely mapped read chenyao Bioinformatics 6 12-10-2012 03:18 AM
negative bwa mapping quality Anney Bioinformatics 4 07-11-2011 02:42 PM
BWA mapping quality scores? kweber2 Genomic Resequencing 2 09-27-2010 04:01 PM
Interpretation of BWA mapping quality christophpale Bioinformatics 0 07-21-2010 04:15 AM
bwa mapping quality totalnew Bioinformatics 6 05-21-2010 05:50 AM

Reply
 
Thread Tools
Old 01-16-2012, 11:32 AM   #1
mdjones66
Junior Member
 
Location: Cambridge, MA

Join Date: Jul 2008
Posts: 3
Question BWA Reports High Mapping Quality for Poorly Mapped Pairs

I realized after I, serendipitously, ran "bwa sampe" on the same identical alignments (i.e. sai files from the same fastq) that the second mate in the pair would almost always have many mismatches. The surprising thing is that a second paired read with as many as 79 out of 101 mismatches could have a high mapping quality.

I am sure this has something to do with the Smith Waterman alignment that is attempted for the second read.

See: http://seqanswers.com/forums/showthread.php?t=14665

I have a few questions:

1) Why does bwa try and rescue reads that don't map well with bwa aln?
2) Why is the mapping quality so high when there are so many mismatches?
3) Is the reported mapping quality at the individual read level or at the pair level?
4) If I use the -s option to disable Smith-Waterman for the unmapped mate will it still use the results of the BW algorithm to get the reads in the pair that map?
mdjones66 is offline   Reply With Quote
Old 01-16-2012, 09:29 PM   #2
nilshomer
Nils Homer
 
nilshomer's Avatar
 
Location: Boston, MA, USA

Join Date: Nov 2008
Posts: 1,285
Default

1) Why does bwa try and rescue reads that don't map well with bwa aln?
Since repetitive hits (or other artifacts) can cause "bwa aln" to miss a valid alignment, so using one end as anchor for the other can improve both sensitivity and specificity.
2) Why is the mapping quality so high when there are so many mismatches?
I am not sure. Could you give an example with the before/after and what you expect?
3) Is the reported mapping quality at the individual read level or at the pair level?
Both, it is is the original mapping quality, adjusted based on how well the pair maps.
4) If I use the -s option to disable Smith-Waterman for the unmapped mate will it still use the results of the BW algorithm to get the reads in the pair
Yes, but try it yourself on a small # of reads to confirm.
nilshomer is offline   Reply With Quote
Reply

Tags
bwa sampe, mapping quality, paired end

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 12:55 AM.


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