SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
Tophat2 very slow when running over Bowtie2 jdenvir Bioinformatics 2 02-18-2013 06:28 AM
tophat2 mdb@wistar Bioinformatics 6 02-04-2013 11:51 AM
tophat2 error Xi Wang Bioinformatics 13 12-21-2012 07:36 AM
bowtie2 vs. Tophat2 RNA-Seq tschauer Bioinformatics 2 12-18-2012 03:45 AM
tophat2/bowtie2 inconsistency in number of unmapped reads manianslab Bioinformatics 2 07-13-2012 01:56 PM

Reply
 
Thread Tools
Old 02-26-2013, 09:38 AM   #1
rnavon
Junior Member
 
Location: Israel

Join Date: Feb 2013
Posts: 6
Default Tophat2 can't find Bowtie2

Hi Everyone,

After my previous installed tophat/bowtie versions worked without a problem, I wanted to update to the newest versions and also installed tophat2 and bowtie2. Both programs have links to them from the /bin directory which is in the path.
When trying to run the running example, tophat2 claims I do not have the correct version of bowtie installed. I'm a UNIX newbie and would appreciate any help and ideas!

Thanks!

Code:
[galaxy01@gene3 test_data]$ 
[galaxy01@gene3 test_data]$ bowtie --version
bowtie version 0.12.5
64-bit
Built on sycamore.umiacs.umd.edu
Sat Apr 24 15:56:29 EDT 2010
Compiler: gcc version 4.1.2 20080704 (Red Hat 4.1.2-46)
Options: -O3 -m64  -Wl,--hash-style=both
Sizeof {int, long, long long, void*, size_t, off_t}: {4, 8, 8, 8, 8, 8}
[galaxy01@gene3 test_data]$ 
[galaxy01@gene3 test_data]$ 
[galaxy01@gene3 test_data]$ bowtie2 --version
/bin/bowtie2-align version 2.1.0
64-bit
Built on igm3
Thu Feb 21 09:33:38 EST 2013
Compiler: gcc version 4.5.4 (GCC) 
Options: -O3 -m64 -msse2 -funroll-loops -g3 
Sizeof {int, long, long long, void*, size_t, off_t}: {4, 8, 8, 8, 8, 8}
[galaxy01@gene3 test_data]$ 
[galaxy01@gene3 test_data]$ 
[galaxy01@gene3 test_data]$ tophat2 --version
TopHat v2.0.7
[galaxy01@gene3 test_data]$ 
[galaxy01@gene3 test_data]$ 
[galaxy01@gene3 test_data]$ tophat2 test_ref reads_1.fq reads_2.fq

[2013-02-26 09:35:20] Beginning TopHat run (v2.0.7)
-----------------------------------------------
[2013-02-26 09:35:20] Checking for Bowtie
Error: TopHat requires Bowtie 2.0.5 or later
[galaxy01@gene3 test_data]$
rnavon is offline   Reply With Quote
Old 02-26-2013, 10:56 AM   #2
GenoMax
Senior Member
 
Location: East Coast USA

Join Date: Feb 2008
Posts: 7,079
Default

Can you unlink (or rename) bowtie (v.1) in /bin temporarily to see if that allows TopHat to recognize the correct version it needs?
GenoMax is offline   Reply With Quote
Old 02-26-2013, 12:15 PM   #3
rnavon
Junior Member
 
Location: Israel

Join Date: Feb 2013
Posts: 6
Default

I'll try that but it's not a permanent solution as I want to be able to keep the previous version for other users.
Can't I have both bowtie and bowtie2 installed side by side?
rnavon is offline   Reply With Quote
Old 02-26-2013, 12:23 PM   #4
GenoMax
Senior Member
 
Location: East Coast USA

Join Date: Feb 2008
Posts: 7,079
Default

Just saw this over at the TopHat site. Perhaps upgrading to latest Tophat may fix your problem.

Quote:
Version 2.0.8 is a quick fix release addressing the following issues:

This version correctly handles the newest version of Bowtie2 v2.1.0.
The segment mapping slow-down introduced by some Bowtie2 parameter changes in version 2.0.7 is now corrected
Quote:
There is also a new version of bowtie2 (v.2.1.0) available as well.

Last edited by GenoMax; 02-26-2013 at 12:30 PM.
GenoMax is offline   Reply With Quote
Old 02-26-2013, 12:27 PM   #5
rnavon
Junior Member
 
Location: Israel

Join Date: Feb 2013
Posts: 6
Default

Quote:
Originally Posted by GenoMax View Post
Just saw this over at the TopHat site. Perhaps upgrading to latest Tophat may fix your problem.
Thanks!
It wasn't on the site a couple of hours ago. I'll install the new tophat version and see if it helps.
rnavon is offline   Reply With Quote
Old 02-27-2013, 07:51 AM   #6
rnavon
Junior Member
 
Location: Israel

Join Date: Feb 2013
Posts: 6
Default

Updating Tophat from 2.0.7 to 2.0.8 solved the problem.
rnavon 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 08:01 AM.


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