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Old 04-27-2016, 12:34 AM   #1
Location: us

Join Date: Apr 2016
Posts: 14
Default TopHat- index file

Hi all!
I am usign TopHat2 and I get this error:
Beginning TopHat run (v2.0.10)
Checking for Bowtie
Bowtie 2 not found, checking for older version..
Bowtie version:
Checking for Samtools
Samtools version:
Checking for Bowtie index files (genome)..
Error: Could not find Bowtie index files (SaccFasta.idx.*.ebwt)

I have read in some forum that the problem is that TopHat didn't find bowtie2. Are there different in the results if I use the index-file of Bowtie1 or Bowtie2?
Thank you in advance
edeka is offline   Reply With Quote
Old 04-27-2016, 04:36 AM   #2
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Location: East Coast USA

Join Date: Feb 2008
Posts: 7,022

Index files for bowtie v.1 and v.2 have different formats so they can't be used interchangeably.

That said I would suggest that you upgrade TopHat to the latest version (v.2.1.1). Also include the full command you are using if you continue having issues.
GenoMax is offline   Reply With Quote
Old 04-27-2016, 07:19 AM   #3
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Location: India

Join Date: Oct 2015
Posts: 2

or use --bowtie1 if you do not wish to use bowtie2, as mentioned in
cpad0112 is offline   Reply With Quote

bowtie, index file, tophat

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