But no plain bowtie2-build (the -l is for 64-bit indexes but they are not supported by TopHat as yet)?
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No, I have a plain bowtie2-build as well.Comment
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I am stumped.
Give a real sample a try to see if that works.Comment
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Damn =P I'll do that and see if it works. Thanks for all your help, regardless!Comment
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Downgrading to Bowtie 2.2.2 did the trick! Must have been a bug or something in 2.2.3...Comment
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I was using Bowtie 2.2.1. Won't upgrade to 2.2.3.Comment
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Error in testing the installation of Tophat
I'm a brand new person in RNA-Seq and a beginner in bioinformatics as well. So my apologies if my question is naïve or it has been posted already. Recently I installed Tophat v2.0.12, with Bowtie, SAMtools and Boost libraries, in Ubuntu 12.04 lts 32-bits. However when I tried to test the installation
tophat -r 20 test_ref reads_1.fq reads_2.fq
I got this error:
[2014-07-04 10:52:25] Beginning TopHat run (v2.0.12)
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[2014-07-04 10:52:25] Checking for Bowtie
Bowtie 2 not found, checking for older version..
Error: TopHat requires Bowtie 0.12.9 or later
It seems to me there is a problem with the version of bowtie I have installed, perhaps to old? If you could please give some clue about how to solve this problem?
Thanks in advancedComment
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If you only have bowtie (v.1.x) installed then you may need to add the following optionOriginally posted by lamaga View Post
It may be better to install bowtie2 (http://sourceforge.net/projects/bowt...les/bowtie2/)?Code:$ tophat --bowtie1 -r 20 test_ref reads_1.fq reads_2.fq
Or it may be a simple fix of adjusting your $PATH so bowtie directories are included there.Last edited by GenoMax; 07-06-2014, 06:21 AM.Comment
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You need the newest version of tophat
TopHat 2.0.12 release 6/24/2014
Version 2.0.12 is a maintenance release with the following simple fix:
This version is compatible with Bowtie2 v2.2.3.Comment
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