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  • #16
    Did anyone fixed the problem? same problem happened here.

    Comment


    • #17
      Cufflinks duplicated genes error

      Hi all,

      I am not sure if this is a 'universal' answer, but the problem i was running into was in the gtf file. Cufflinks does not deal well with duplicated genes ID. In my particular case, i was using an old gtf file that must have had duplicates. Once i used the most updated one, i had no problem.

      G

      Comment


      • #18
        Originally posted by Gonza View Post
        Hi all,

        I am not sure if this is a 'universal' answer, but the problem i was running into was in the gtf file. Cufflinks does not deal well with duplicated genes ID. In my particular case, i was using an old gtf file that must have had duplicates. Once i used the most updated one, i had no problem.

        G
        Hi, do you mean the duplicated gene ID in the reference gtf file or the gtf file generated by cufflinks? Also was your reference gtf file sorted? Can you please send me a screenshot of the gtf file that works and that doesn't work?

        Thank you very much!

        Comment


        • #19
          Hi,

          This is what i was getting.



          [Fri Jan 6 12:35:41 2017] Beginning transcriptome assembly merge

          -------------------------------------------

          [Fri Jan 6 12:35:41 2017] Preparing output location ./merged_asm/

          [Fri Jan 6 12:36:23 2017] Converting GTF files to SAM

          [12:36:23] Loading reference annotation.

          GFF Error: duplicate/invalid 'transcript' feature ID=Peaxi162Scf00002g00014.1

          [FAILED]

          Error: could not execute gtf_to_sam




          Once i started to used an updated GTF/GFF file i had no problem. Not sure what species you're working with, but this problem will not occur if you are using one with well annotated features.

          Good luck

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          • #20
            It turned out my problem was caused by the reference gtf/gff file too. Thank you very much!

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            • #21
              glad it worked!

              Comment

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