SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
Problem with BWA mapping of Illumina PE short insert size fragments (FFPE material) LadyGray Bioinformatics 2 10-22-2012 01:20 AM
BWA behaviour with Mate Pair data + Multi read mapping apratap Bioinformatics 5 06-23-2011 04:38 PM
Illumina mapping with bwa bpetersen Bioinformatics 5 03-14-2011 11:04 PM
BWA mapping against hg18 seq_GA Bioinformatics 7 05-31-2010 06:48 PM
BWA and Velvet : Anamolies in contigs and read mapping to reference apratap Bioinformatics 1 01-29-2010 12:44 PM

Reply
 
Thread Tools
Old 10-11-2011, 07:34 AM   #1
pbluescript
Senior Member
 
Location: Boston

Join Date: Nov 2009
Posts: 224
Default Problem with BWA mapping second read

I am mapping some 2X100PE RNA-Seq data and BWA is mapping the second read very oddly for some of my samples.
I am testing out a mix of BWA and Tophat for mapping the reads and sometimes BWA will say two reads in a pair map to the same location even though the second read is filled with mismatches. I have attached an example IGV screenshot showing the BWA+Tophat mapped reads on the top and the Tophat only mapped reads on the bottom.
This happens for some of the samples, but not for others, even though the libraries were all prepared the same way. The coverage graphs on the top are identical, and since it is FPKM, there isn't likely to be much effect when it comes to differential expression analysis. Indeed, when comparing the sample mentioned above mapped with either BWA+Tophat or just Tophat, the R-squared is 0.9705.
I was planning on playing around with the BWA settings a bit, but I thought I'd pose the problem here to see if anyone had some suggestions.
Attached Images
File Type: jpg 3UTRcomparison.jpg (83.2 KB, 25 views)
pbluescript is offline   Reply With Quote
Old 10-11-2011, 07:44 AM   #2
prm36
Member
 
Location: Edinburgh

Join Date: Mar 2010
Posts: 16
Default

I find that by running bwa sampe with the -s option, the second read of the pair does not get mapped, and thus resolves this issue.
prm36 is offline   Reply With Quote
Old 10-11-2011, 07:52 AM   #3
prm36
Member
 
Location: Edinburgh

Join Date: Mar 2010
Posts: 16
Default

I just checked my lab book for my notes for when I found myself having the same problem.

"""
Reads with multiple mismatches are mapping.
If one read of a pair maps, SW algorithm in bwa will map pair regardless whether paired read passes mismatch filter or not.
Workaround
Run bwa aln with -n 1 (allow 1 mismatch per read)
Run bwa sampe with -s (disable SW algorithm)
"""
prm36 is offline   Reply With Quote
Old 10-12-2011, 07:52 AM   #4
pbluescript
Senior Member
 
Location: Boston

Join Date: Nov 2009
Posts: 224
Default

Thanks for the advice prm36. Unfortunately, it didn't seem to help. I get identical numbers of reads mapping and the same problem when I use the -s option with bwa.

Any other suggestions?
pbluescript 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 10:07 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO