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  • fraca
    Junior Member
    • Mar 2013
    • 8
    #1

    GFF to GFF3

    Hi,
    I'm looking for a program that converts GFF (General Feature Format) files into to GFF3. I have see other post tht talk about it but without any solution.
    Thanks,

    Marco
    Tags: None
  • blancha
    Senior Member
    • May 2013
    • 367
    #2
    Your post makes no sense since GFF3 is a version of GFF.

    If you want to convert a GTF (sometimes known as GFF 2.5) file to GFF3, you can try the following program. The program can be run both through a web portal, and as a stand-alone Perl script.
    http://www.sequenceontology.org/cgi-bin/converter.cgi


    The one occasion where I absolutely needed a GFF3 file was for the program MISO. I just downloaded the UCSC table, and used a script provided on the MISO website to convert it to the GFF3 format.
    404 — Christopher Burge Laboratory
    http://genes.mit.edu/burgelab/miso/scripts/ucsc_table2gff3.pl
    Last edited by blancha; 11-20-2014, 04:06 PM.

    Comment

    • fraca
      Junior Member
      • Mar 2013
      • 8
      #3
      Thanks a lot, I have download the Perl script and work perfetctly. I need the GFF3 file for do population genomic analysis with NPStat (https://code.google.com/p/npstat/) that work with pooled sequencing data.

      Marco

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