SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
bowtie index location question martinobarenco Bioinformatics 17 02-27-2016 05:58 PM
Tophat2: Error running bowtie: JonB Bioinformatics 5 01-18-2014 03:09 AM
tophat2 bowtie option help akh22 Bioinformatics 3 11-26-2013 03:24 AM
TOPHAT / TOPHAT2 checking bowtie version error? jmt Bioinformatics 3 11-05-2012 08:31 AM
cDNA or protein location to genomic DNA location Liam_Gallagher Bioinformatics 5 05-11-2012 02:34 AM

Reply
 
Thread Tools
Old 02-12-2014, 06:46 AM   #1
lucro
Junior Member
 
Location: ohio

Join Date: Feb 2014
Posts: 3
Default Tophat2 bowtie location

Hello all,

After installing Bio Linux and running the test data: it says that I don't have bowtie2 but bowtie2 by itself is working just fine.

What is the default location that Tophat 2 accesses Bowtie2 from? Also, is there a way to change the paths that Tophat 2 accesses it's external binaries from after Tophat 2 has already been compiled? (Samstools, Boost, Bowtie etc)?


Thanks, any constructive responses will be greatly appreciated.
I've spent a lot of time on this but I'm just hitting my head against the wall.
lucro is offline   Reply With Quote
Old 02-12-2014, 06:52 AM   #2
dpryan
Devon Ryan
 
Location: Freiburg, Germany

Join Date: Jul 2011
Posts: 3,480
Default

I think it just looks in your PATH. Are the appropriate directories in there?
dpryan is offline   Reply With Quote
Old 02-12-2014, 07:50 AM   #3
lucro
Junior Member
 
Location: ohio

Join Date: Feb 2014
Posts: 3
Default

Quote:
Originally Posted by dpryan View Post
I think it just looks in your PATH. Are the appropriate directories in there?
Appropriate directories within bowtie2? Everything appears to be there. I exported the path below:

export PATH=/usr/local/bowtie2-2.2.2.0:$PATH


tophat -r tophat -r 20 test_ref reads_1.fq reads_2.fq
...
Error: Tophat requires Bowtie 0.12.9 or later
lucro is offline   Reply With Quote
Old 02-12-2014, 07:54 AM   #4
dpryan
Devon Ryan
 
Location: Freiburg, Germany

Join Date: Jul 2011
Posts: 3,480
Default

What version of tophat are you using? It seems to be one that defaults to bowtie1 whereas you have bowtie2. The easiest fix would be to just upgrade your tophat version (the most recent versions should default to using bowtie2 instead of bowtie1). While bowtie1 and bowtie2 are both "bowtie", their syntax and everything is very different so you can't just arbitrarily mix and match them.
dpryan is offline   Reply With Quote
Old 02-12-2014, 08:20 AM   #5
lucro
Junior Member
 
Location: ohio

Join Date: Feb 2014
Posts: 3
Default

Quote:
Originally Posted by dpryan View Post
What version of tophat are you using? It seems to be one that defaults to bowtie1 whereas you have bowtie2. The easiest fix would be to just upgrade your tophat version (the most recent versions should default to using bowtie2 instead of bowtie1). While bowtie1 and bowtie2 are both "bowtie", their syntax and everything is very different so you can't just arbitrarily mix and match them.
I really appreciate the quick replies, dpryan.

I'm using Tophat v2.0.8 and bowtie2.2.0. I'll see if updating Tophat works.

Thanks
lucro is offline   Reply With Quote
Reply

Tags
bowtie 2, tophat 2

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 08:08 PM.


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