SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
Bowtie 2 multiple alignment default mode: how the best one is chosen? sbcn Bioinformatics 3 12-03-2012 07:23 AM
Bowtie 2 parameters chedonat Bioinformatics 2 03-30-2012 06:20 AM
bfast default parameters jy123 Bioinformatics 1 06-04-2011 08:42 PM
Bowtie parameters khb Bioinformatics 11 12-16-2010 09:08 PM
Recommended Bowtie Parameters agc SOLiD 0 05-10-2010 03:44 AM

Reply
 
Thread Tools
Old 01-23-2014, 07:17 AM   #1
ThePresident
Member
 
Location: Sherbrooke / Canada

Join Date: Jun 2012
Posts: 72
Default Bowtie default parameters

Hello,

I have a very simple question about bowtie:

If I run bowtie without explicitly specifying the mode, the default mode should be used (which is -n mode), right? Now, if I don't specify neither the number of mismatches (-N) nor seed length (-L), what are the default parameters for N and L then?

Thank you in advance,

TP
ThePresident is offline   Reply With Quote
Old 01-23-2014, 07:33 AM   #2
GenoMax
Senior Member
 
Location: East Coast USA

Join Date: Feb 2008
Posts: 7,060
Default

For bowtie2

-N <int> max # mismatches in seed alignment; can be 0 or 1 (0)
-L <int> length of seed substrings; must be >3, <32 (22)

N = 0 and L = 22.
Quote:
Presets: Same as:
For --end-to-end:
--very-fast -D 5 -R 1 -N 0 -L 22 -i S,0,2.50
--fast -D 10 -R 2 -N 0 -L 22 -i S,0,2.50
--sensitive -D 15 -R 2 -N 0 -L 22 -i S,1,1.15 (default)
--very-sensitive -D 20 -R 3 -N 0 -L 20 -i S,1,0.50

For --local:
--very-fast-local -D 5 -R 1 -N 0 -L 25 -i S,1,2.00
--fast-local -D 10 -R 2 -N 0 -L 22 -i S,1,1.75
--sensitive-local -D 15 -R 2 -N 0 -L 20 -i S,1,0.75 (default)
--very-sensitive-local -D 20 -R 3 -N 0 -L 20 -i S,1,0.50
GenoMax is offline   Reply With Quote
Old 01-23-2014, 07:36 AM   #3
ThePresident
Member
 
Location: Sherbrooke / Canada

Join Date: Jun 2012
Posts: 72
Default

Yeah, that's for bowtie 2. I used the original version of bowtie. I wonder if they kept the same default parameters...
ThePresident is offline   Reply With Quote
Old 01-23-2014, 07:45 AM   #4
mastal
Senior Member
 
Location: uk

Join Date: Mar 2009
Posts: 667
Default

The default values of n and l for bowtie are different.

See the bowtie manual

http://bowtie-bio.sourceforge.net/ma...alignment-mode
mastal is offline   Reply With Quote
Old 01-23-2014, 07:46 AM   #5
GenoMax
Senior Member
 
Location: East Coast USA

Join Date: Feb 2008
Posts: 7,060
Default

N and L are not valid options for bowtie 1.0 (but n and l are)

Quote:
-n/--seedmms <int> max mismatches in seed (can be 0-3, default: -n 2)
-e/--maqerr <int> max sum of mismatch quals across alignment for -n (def: 70)
-l/--seedlen <int> seed length for -n (default: 28)
GenoMax is offline   Reply With Quote
Old 01-23-2014, 07:49 AM   #6
ThePresident
Member
 
Location: Sherbrooke / Canada

Join Date: Jun 2012
Posts: 72
Default

Quote:
Originally Posted by GenoMax View Post
N and L are not valid options for bowtie 1.0 (but n and l are)
Darn, I was looking at wrong place... Anyway, thanks alot!

TP
ThePresident is offline   Reply With Quote
Reply

Tags
bowtie

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 08:38 PM.


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