SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
How to get uniquely mapped reads from Tophat subeet Bioinformatics 10 11-28-2012 05:56 AM
filtering for uniquely mappable regions dphansti Bioinformatics 9 10-13-2011 04:35 PM
not uniquely mapped reads unidodo RNA Sequencing 2 04-22-2011 02:07 PM
BWA Uniquely Mapped Reads NF_seq Bioinformatics 0 09-06-2010 03:32 AM
DEGseq and uniquely mapped reads PFS Bioinformatics 1 07-14-2010 09:37 AM

Reply
 
Thread Tools
Old 12-09-2010, 02:38 PM   #1
Protaeus
Member
 
Location: 86001

Join Date: Aug 2010
Posts: 21
Default ID'ing Uniquely Mapped Regions in BWA

I have another BWA inquiry. How can one id the uniquely mapped reads from a sam/bam generated by BWA? Thanks for any thoughts.
Protaeus is offline   Reply With Quote
Old 12-09-2010, 03:52 PM   #2
dawe
Senior Member
 
Location: 4530'25.22"N / 915'53.00"E

Join Date: Apr 2009
Posts: 258
Default

Quote:
Originally Posted by Protaeus View Post
I have another BWA inquiry. How can one id the uniquely mapped reads from a sam/bam generated by BWA? Thanks for any thoughts.
They have XT tag set to "U".
dawe is offline   Reply With Quote
Old 12-10-2010, 02:31 AM   #3
epigen
Senior Member
 
Location: Germany

Join Date: May 2010
Posts: 101
Default

You can use samtools view -q 1 to only output uniquely mapped reads (and omit both unmapped and ambiguous ones). Ambiguous reads that can be mapped to different locations with the same score have mapping quality 0 in BWA.
epigen 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 07:30 AM.


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