SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
Bfast localalign error dg.pooja General 1 01-31-2011 06:35 PM
bfast localalign error nimmi Bioinformatics 6 01-05-2011 09:40 AM
bfast localalign issues yy01 Bioinformatics 8 12-15-2010 12:19 AM
bfast localalign looking for the wrong reference file baldeberre Bioinformatics 16 09-17-2010 02:56 PM
BFAST match/localalign help Esther Bioinformatics 3 08-04-2010 06:19 AM

Reply
 
Thread Tools
Old 09-17-2010, 10:13 AM   #1
Protaeus
Member
 
Location: 86001

Join Date: Aug 2010
Posts: 21
Default bfast localalign -U option?

Hello,

What are the downsides of using the -U option at the bfast localalign step? I presume it'll be more computationally expensive, but are there things with the resulting data that would be of concern?
Protaeus is offline   Reply With Quote
Old 09-17-2010, 12:11 PM   #2
nilshomer
Nils Homer
 
nilshomer's Avatar
 
Location: Boston, MA, USA

Join Date: Nov 2008
Posts: 1,285
Default

Quote:
Originally Posted by Protaeus View Post
Hello,

What are the downsides of using the -U option at the bfast localalign step? I presume it'll be more computationally expensive, but are there things with the resulting data that would be of concern?
When not using the '-U', bfast enforces that where the seeds/masks match the reference during 'bfast match' also match the reference in the final alignment. This is a constrained Smith Waterman alignment, which speeds up the local alignment. Using the '-U' option ignores those constraints.

The philosophical question that the '-U' option lets one ask is if we get to a 100bp window in a 3Gb genome, should we constrain the alignment based on how we got there?
nilshomer is offline   Reply With Quote
Old 09-17-2010, 12:50 PM   #3
Protaeus
Member
 
Location: 86001

Join Date: Aug 2010
Posts: 21
Default

That brings up a separate but related question I had. A lot of my recent illumina runs have been 101bp on bacterial genomes. Generally speaking, the key width for my indexes is 30. Would there be any reason to believe I would benefit from trying a larger key width? Or is this where the -U option in localalign might be helpful?
Protaeus 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 06:15 AM.


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