TopHat- index file

[edeka]

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: 1.1.2.0
Checking for Samtools
Samtools version: 0.1.19.0
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

[GenoMax]

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.

[cpad0112]

or use --bowtie1 if you do not wish to use bowtie2, as mentioned in https://ccb.jhu.edu/software/tophat/tutorial.shtml.