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  • #16
    could not locate bowtie index corresponding to biobase "e_coli"

    Hi,

    I am trying to use bowtie from my environmental variable-
    $ Module load bio/bowtie/1.1.2
    $ bowtie e_coli reads/e_coli_1000.fq
    But it returns me the following:
    Could not locate a Bowtie index corresponding to basename "e_coli"
    Command: bowtie --wrapper basic-0 e_coli reads/e_coli_1000.fq

    I thought e_coli indices comes with the package - so this this should be a easy command to run.
    Could someone guide me about what is the right command?

    Comment


    • #17
      Environment modules only put the executable in the PATH, nothing more. You'll still need to tell bowtie where the indices are (assuming they were even installed).

      Comment


      • #18
        Thank you so much! I had to specify my home directory for the genome and the read file.

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