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  • edeka
    Member
    • Apr 2016
    • 14
    #1

    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: 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
    Tags: bowtie, index file, tophat
  • GenoMax
    Senior Member
    • Feb 2008
    • 7142
    #2
    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.

    Comment

    • cpad0112
      Junior Member
      • Oct 2015
      • 2
      #3
      or use --bowtie1 if you do not wish to use bowtie2, as mentioned in https://ccb.jhu.edu/software/tophat/tutorial.shtml.

      Comment

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