Convert cufflinks GTF to GFF

[seq_newbie]

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.

[Emilie]

You can try this converter from Sequence Ontology:

http://song.cvs.sourceforge.net/viewvc/song/software/scripts/gtf2gff3/

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

[kwatts59]

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.