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  • problem with tophat commnd directing bowtie indexes

    here is the command I given. I directed bowtie indexes but not working

    I downloaded hg18 index from bowtie ftp site and unzipped in index folder of bowtie by creating a sub directory hg18.
    Hope I did every thing correct?

    Code:
    [B] tophat -r 200 /home/bogugk/rnaseq/software/bowtie-0.12.5/indexes/hg18 SL001_R00089_RHE011_01pgx2_F3.csfasta SL001_R00089_RHE012_01pgx2_F3.csfasta SL001_R00089_RHE013_01pgx2_F3.csfasta SL001_R00089_RHE014_01pgx2_F3.csfasta SL004_R00058_RHE015_01pgx2_F3.csfasta [/B]
    
    [Wed Jun 16 18:12:39 2010] Beginning TopHat run (v1.0.13)
    -----------------------------------------------
    [Wed Jun 16 18:12:39 2010] Preparing output location ./tophat_out/
    [Wed Jun 16 18:12:39 2010] Checking for Bowtie index files
    Error: Could not find Bowtie index files /home/bogugk/rnaseq/software/bowtie-0.12.5/indexes.*
    Traceback (most recent call last):
      File "/home/bogugk/rnaseq/software/tophat-1.0.13/bin/tophat", line 1635, in ?
        sys.exit(main())
      File "/home/bogugk/rnaseq/software/tophat-1.0.13/bin/tophat", line 1556, in main
        (ref_fasta, ref_seq_dict) = check_index(bwt_idx_prefix)
      File "/home/bogugk/rnaseq/software/tophat-1.0.13/bin/tophat", line 634, in check_index
        check_bowtie_index(idx_prefix)
      File "/home/bogugk/rnaseq/software/tophat-1.0.13/bin/tophat", line 569, in check_bowtie_index
        exit(1)
    TypeError: 'str' object is not callable
    FYI: I also exported index path to .bashrc by plaing this command in .bashrc
    Code:
    export PATH=$PATH:/home/bogugk/rnaseq/software/bowtie-0.12.5/indexes
    /hg18
    Please let me know any suggestions.
    Thanx

  • #2
    As far as I know you don't create a subdirectory for each index. just place the 6 hg18 files in the indexes directory.

    Comment


    • #3
      "/home/bogugk/rnaseq/software/bowtie-0.12.5/indexes/hg18"

      That is wrong

      You should point the the bowtie-base, rather than the directory.

      eg. something like

      "/home/bogugk/rnaseq/software/bowtie-0.12.5/indexes/hg18/genome"
      SpliceMap: De novo detection of splice junctions from RNA-seq
      Download SpliceMap Comment here

      Comment

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