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  • gaurav
    Junior Member
    • Oct 2013
    • 3

    Tophat trouble

    Hi there,

    I am having trouble with my tophat command for NGS data analysis. The commands I have been using are:

    export PATH=/opt/bowtie-0.12.8:$PATH
    mkdir bowtie_index
    bowtie-build TAIR10.20.dna.toplevel.fa bowtie_index
    export PATH=/opt/tophat/bin/:$PATH
    export PATH=/opt/samtools-0.1.17/bin:$PATH
    tophat -i 40 -I 1000 -G TAIR10.20.gtf -o ./tophat.out_arib3 bowtie_index SRR548277.fastq


    The output files I am getting are a fa file, sam file, bam file, and lots of z- files. However, I am not getting any accepted hits or bed files.

    I would highly highly appreciate if anyone please help me solving the problem.

    Thanks
    G
  • dpryan
    Devon Ryan
    • Jul 2011
    • 3478

    #2
    Did it actually run to completion or did it die at some point? I assume the latter. What are the names of the files that it did create?

    Comment

    • gaurav
      Junior Member
      • Oct 2013
      • 3

      #3
      Hi dpryan,

      Thanks for your reply.

      Tophat is running to complete and the files it is outputting are:

      stub_header.sam
      practice.fa
      practice.bwt.samheader.sam
      left_kept_reads_seg4.fq.z
      left_kept_reads_seg3.missing.fq.z
      left_kept_reads_seg3.fq.z
      left_kept_reads_seg3.bwtout.z
      left_kept_reads_seg2.missing.fq.z
      left_kept_reads_seg2.fq.z
      left_kept_reads_seg2.bwtout.z
      left_kept_reads_seg1.missing.fq.z
      left_kept_reads_seg1.fq.z
      left_kept_reads_seg1.bwtout.z
      left_kept_reads_missing.fq.z
      left_kept_reads.unspl.bam
      left_kept_reads.fq.z
      left_kept_reads.bwtout.z
      24594.bwt_unmapped.z.fifo

      Thanks for your help.

      Comment

      • dpryan
        Devon Ryan
        • Jul 2011
        • 3478

        #4
        That looks a lot like it aborted before finishing. There's probably a "log" directory or something like that. Have a look at the run log in there to see if you can discern where things stopped.

        Comment

        • gaurav
          Junior Member
          • Oct 2013
          • 3

          #5
          Hey dpryan,
          You were right, it was just an issue of being stopped in halfway (I was using a cluster for running it and been logged off in between).. Anyways, it ran properly now and got requisite files ..

          Thanks for your help again.

          G

          Comment

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