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  • TopHat Error: Could not find Bowtie index files /bowtie-0.12.5/indexes/.

    Hello all,

    I am using TopHat for the first time and it does not find my bowtie indexes. I have an old version of Bowtie installed; all the indexes that I need are there (I used it before, no problem). When I run TopHat, it gives the following error:

    tophat -r 20 /bowtie-0.12.5/indexes /data_with_reads/sequence.txt

    Error: Could not find Bowtie index files /bowtie-0.12.5/indexes/.*
    This directory actually contains all the bowtie indexes (all genomes that I used before). Should I reformat/rename/reorganize this old bowtie directory somehow?

    Any help?
    Thanks!

  • #2
    The problem is that you need to specify in the command the name of the bowtie index in addition to the folder.

    So, something like this instead:
    Code:
    tophat -r 20 /bowtie-0.12.5/indexes/genome_file_name /data_with_reads/sequence.txt

    Comment


    • #3
      Originally posted by NM_010117 View Post
      The problem is that you need to specify in the command the name of the bowtie index in addition to the folder.

      So, something like this instead:
      Code:
      tophat -r 20 /bowtie-0.12.5/indexes/genome_file_name /data_with_reads/sequence.txt
      Thank you for the suggestion. Do you know which of the following files in the indexes directory should be specified?

      hg18.1.ebwt
      hg18.2.ebwt
      hg18.3.ebwt
      hg18.4.ebwt
      hg18.rev.2.ebwt
      hg18.rev.1.ebwt

      Comment


      • #4
        You actually won't specify a file, but rather the base file name. So, in this case your command would be:
        Code:
        tophat -r 20 /bowtie-0.12.5/indexes/hg18 /data_with_reads/read_1.fastq /data_with_reads/read_2.fastq

        Comment


        • #5
          Just "hg18", without the quotes. From the TopHat manual, you just specify the "basename", which I recall being hg18, or mm9, or whatever you're using. You can then set the PATH in the BOWTIE_INDEXES environment variable. If you're using bash:
          Code:
          export BOWTIE_INDEXES=/bowtie-0.12.5/indexes
          then you should be able to run your alignments:
          Code:
          tophat -r 20 hg18 /path/to/reads.fastq
          You can also set the BOWTIE_INDEXES variable in your .bashrc (or equivalent) if you'll be doing this often.

          Comment


          • #6
            NM_010117, dpryan,
            Thank you, this helped!

            Comment


            • #7
              Thank you, NM 010117. Your answer to rebrendi helped me.

              Comment


              • #8
                Originally posted by dpryan View Post
                Just "hg18", without the quotes. From the TopHat manual, you just specify the "basename", which I recall being hg18, or mm9, or whatever you're using. You can then set the PATH in the BOWTIE_INDEXES environment variable. If you're using bash:
                Code:
                export BOWTIE_INDEXES=/bowtie-0.12.5/indexes
                then you should be able to run your alignments:
                Code:
                tophat -r 20 hg18 /path/to/reads.fastq
                You can also set the BOWTIE_INDEXES variable in your .bashrc (or equivalent) if you'll be doing this often.
                Hi,

                Is there a command line option to specify the bowtie index path? Our indexes are stored in a different location from bowtie and have different names from the ususal. Using the methods you listed tophat --fusion... still cannot find its indexes --no matter what path and filename I list.

                Joe White

                Comment


                • #9
                  You can just specify the path along with the base, so "/I'm/some/random/path/some_base" will work.

                  Comment


                  • #10
                    *All* index files with that specific base name have to be in the path (directory) that Devon mentions above.

                    Comment


                    • #11
                      tophat --color --quals fr-secondstrand Bowtie-directory/BOWTIE/ebwt_base -o NGR1_NGR2_1_thout genome NFN_run6_Transcriptoma_29102013_bcSample1_F3_NGR1.csfasta NFN_run6_Transcriptoma_29102013_bcSample1_F3_NGR2.csfasta NFN_run6_Transcriptoma_29102013_bcSample1_F3_QV_NGR1.qual NFN_run6_Transcriptoma_29102013_bcSample1_F3_QV_NGR2.qual

                      Beginning TopHat run (v2.1.0)
                      Checking for Bowtie
                      Bowtie version: 1.1.1.0
                      [2016-06-22 13:23:45] Checking for Bowtie index files (genome)..
                      Error: Could not find Bowtie index files (fr-secondstrand.*.ebwt)

                      the bowtie don't find the file index!

                      Comment


                      • #12
                        Look at the actual error message. Sure, it says it can't find them, but look at the names of what you're telling it your indexes are called. Hint: you can't just randomly put "fr-secondstrand" anywhere in the command.

                        Comment

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