SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
BWA and sub-optimal alignments LauraR Bioinformatics 0 02-10-2012 08:46 AM
How many multiple alignments to allow? hlwright Bioinformatics 0 04-14-2011 12:40 AM
BWA: suboptimal alignments ElMichael Bioinformatics 2 03-29-2011 02:31 PM
merging bwa alignments arnkas Genomic Resequencing 5 07-07-2010 08:26 AM
BWA alignments and time cggj Bioinformatics 5 05-13-2010 11:41 AM

Reply
 
Thread Tools
Old 08-07-2011, 12:37 PM   #1
efoss
Member
 
Location: Seattle

Join Date: Jul 2011
Posts: 98
Default multiple alignments with BWA

The manuscript "Fast and accurate short read alignment with Burrows–Wheeler transform" says this:

"It [BWA] performs gapped alignment for single- end reads, supports paired-end mapping, generates mapping quality and gives multiple hits if required."

I would like to use identify all reasonable alignments for my reads, since if I see a read aligning to many places in the genome, I know to be skeptical of that alignment. However, I don't see this option in BWA. Can anyone help me out here?

Thanks.

Eric
efoss is offline   Reply With Quote
Reply

Tags
bwa, multiple alignments, multiple hits

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 04:58 PM.


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