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  • Convert cufflinks GTF to GFF

    Hi,

    I am trying to convert a cufflinks GTF file (transcripts.gtf) to a GFF3 file. I have minimal Perl and Python and would not have a clue where to even begin. Someone sent me a python code that works for GTF annotation files but this does not work for the cufflinks file (just outputs an empty file). If anyone has a script to achieve this it would be greatly appreciated.

    Regards,

    K.

  • #2
    You can try this converter from Sequence Ontology:
    The world's largest development and download repository of Open Source code and applications

    To make it work on Cufflinks *.gtf files you should un-comment a line at the end of the configuration file gtf2gff3.cfg (unless you will have an error message which says that "." is an invalid strand):

    #Use the following value (+ or -) for a features strand as the default if an invalid value is passed.
    DEFAULT_STRAND = +

    Emilie

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    • #3
      Why do you want to convert GTF to GFF3?
      They are very similar files. The only difference is the 9th column in the GTF file must contain the gene_id and transcript_id fields.

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