SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
Zorro: The Masked Assembler (first public release) glacerda Bioinformatics 3 04-16-2011 05:11 AM
Splitting fasta AND quality on masked sequence mucku Bioinformatics 3 12-15-2010 11:53 AM
why consed finds discrepancies with masked n sequence alig Illumina/Solexa 3 06-12-2009 12:32 PM
Masked/Unmasked Reference Genome ytmnd85 General 5 05-31-2009 03:52 PM
Masked or unmasked genome for ChIP-seq analysis? hbbio Bioinformatics 3 04-07-2009 11:14 AM

Reply
 
Thread Tools
Old 11-08-2009, 11:45 PM   #1
rand
Junior Member
 
Location: Sweden, Stockholm

Join Date: Jul 2009
Posts: 4
Default bwa masked sequence?

Does anyone know if BWA is handling masked sequences properly? I'm having a problem where I find some reads aligned to genome gaps. I have tried converting the N's to X's, but still encountering the same problem.
rand is offline   Reply With Quote
Old 11-09-2009, 05:01 AM   #2
lh3
Senior Member
 
Location: Boston

Join Date: Feb 2008
Posts: 693
Default

This is a known issue. Ambiguous bases are converted to random sequences. If you use bwa-short, the XN tag tells you how many "N" in the alignment. If you use bwasw, you do not get this information, but you may find such hits by checking you reference genome.

The chance of a good alignment arising from random hits is vanishingly small. Just ignore those hits.
lh3 is offline   Reply With Quote
Old 11-09-2009, 06:02 AM   #3
rand
Junior Member
 
Location: Sweden, Stockholm

Join Date: Jul 2009
Posts: 4
Default thanks

Thanks!

I just want to add that the N's in my sequence are not for ambigious bases, they represent a sequence gap of unknown size.. So basically its a long stretch [ATGC]+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN[ATGC]+

Last edited by rand; 11-09-2009 at 07:08 AM.
rand is offline   Reply With Quote
Reply

Tags
bwa

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 02:01 AM.


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