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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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)
-----------------------------------------------
[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 advanced
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Originally posted by lamaga View PostI got this error:
[2014-07-04 10:52:25] Beginning TopHat run (v2.0.12)
-----------------------------------------------
[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 advanced
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.
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