SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
BWA errors after quality trimming flipwell Bioinformatics 3 05-21-2012 07:39 PM
Locating individual reads in alignment Tectona Bioinformatics 7 01-17-2012 12:53 AM
Errors from Picard and GATK on a BWA paired-end BAM oiiio Bioinformatics 2 12-07-2011 07:50 PM
TOPHAT ,Error locating program: prep_reads chenyao Bioinformatics 2 08-17-2011 04:34 AM
BWA Alignment Errors Seq1234 Bioinformatics 0 12-15-2009 08:59 PM

Reply
 
Thread Tools
Old 11-03-2009, 02:18 AM   #1
maasha
Senior Member
 
Location: Denmark

Join Date: Apr 2009
Posts: 153
Default Locating homopolymeric errors with BWA

I have a bunch of contigs assembled from 454 data. I also have a stack of Solexa reads from the same organism, and I would like to locate and correct homoplymeric errors using the Solexa reads. Now, using BWA with default options give me a big pile of hits. Inspecting the CIGAR field I find roughly the same amount of insertions and deletions - that was a bit surprising as I expected more deletions (homopolymers)?

Also, I don't see any mismatches - the SAM format description of CIGAR is unclear on this point. How do I locate mismatches?

What do other people do for cleaning homopolymeric errors?



Martin
maasha 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 12:01 AM.


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