SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
Bowtie2 --score-min calculation kristian_ullrich Bioinformatics 2 11-04-2015 11:36 PM
Bowtie2 --score-min option versus default alignment Pradhaun Bioinformatics 4 02-22-2015 12:00 PM
Meaning of Negative Alignment Score in BOWTIE2 output foolishbrat Bioinformatics 4 01-29-2014 04:06 AM
bowtie2 minimum score threshold owenman Bioinformatics 4 08-31-2012 03:59 PM
bowtie2 read length in score-min okyoon Bioinformatics 0 04-09-2012 08:53 AM

Reply
 
Thread Tools
Old 01-04-2016, 05:47 PM   #1
capricy
Senior Member
 
Location: 63130

Join Date: Apr 2012
Posts: 125
Default confused by bowtie2 alignment score

Hello, there,

I am using default mode for bowtie2 reporting and the manual has it "Bowtie 2 does not garantee that the alignment reported is the best possible in terms of alignment score"


The manual also has: It will eventually stop looking, ... or because it already knows all it needs to know to report an alignment

I am really confused by these sentences... Does it mean that other than the reported alignment, the one with better alignment score might be exist?

Thanks for any input!!
capricy is offline   Reply With Quote
Old 01-04-2016, 07:52 PM   #2
tirohia
Member
 
Location: Auckland, NZ

Join Date: Nov 2011
Posts: 46
Default

Others may correct me if I'm wrong, but I've always understood that to be yes, there might exist an alignment with a better score. It finds the best alignment it can given the constraints on it - those being either

a) the number of seed extensions that fail and the number of reseed attempts (the -D and -R options in the manual right under the bit you're quoting)

or b) some other constraint, like if you have set -k 2 which asks bowtie2 to return 2 alignments. Once it's found 2 alignments, it knows all it needs to know to report and thus does so.

There has to be some constraints on the search, if there wasn't it could take a long, long time to finish.

Ben.
tirohia 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 01:57 PM.


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