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  • all_your_base
    Member
    • Mar 2012
    • 40
    #1

    miRDeep-P: getting the scripts to work

    Hi all,

    I've been playing with miRDeep-P recently, and have trouble even getting started. In particular, their script fetch_extended_precursors.pl is completing within a couple of seconds and returns no output.

    This scripts takes the genome reference file and the miRNA .gff file and extends the precursors by 500nt up and downstream from the annotated site. I could write my own to accomplish this, but would like to use the miRDeep-P package as a whole the first time through.

    If anyone has had similar experiences, please let me know!
    Tags: mirdeep, mirdeep-p, mirna, precursor
  • csmatyi
    Member
    • Oct 2011
    • 25
    #2
    we got it to run

    We got the whole pipeline to run. Did you use an appropriate gff file and genome sequence file? What species are you studying? Maybe they have an appropriate species gff file for you on the mirdeep website.

    Comment

    • Latifa77
      Junior Member
      • Sep 2013
      • 6
      #3
      hi,
      did you get good results employing mirdeep-p?

      Comment

      • jack84
        Junior Member
        • Mar 2013
        • 3
        #4
        Another tool for plant miRNA prediction: https://github.com/hangelwen/miR-PREFeR .

        Comment

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