Question

Cufflinks GTF To Gbrowse GFF3

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12.3 years ago

Gregor Rot ▴ 540

Which script do you use to convert cufflinks GTF output to GFF3 output suitable to upload to Gbrowse?

cufflinks gff3 • 16k views

ADD COMMENT • link updated 10.2 years ago by Daniel Standage 4.1k • written 12.3 years ago by Gregor Rot ▴ 540

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You want a script/tool for your work and just wanna do comparisons

ADD REPLY • link 12.3 years ago by Sukhi Singh 11k

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I found gtf2gff3.pl, but it hangs at cufflinks output that contains "." as strand, so i am thinking what to do with those transcripts now.

ADD REPLY • link 12.3 years ago by Gregor Rot ▴ 540

score 15 · Answer 1 · 2013-07-28

I know this is an old question but I just found it on Google so here's the answer: Cufflinks comes with a tool called "gffread" which can transform the gtf-output to gff3. Usage is:

gffread -E merged.gtf -o- > merged.gff3

This will warn you about any errors ("-E") and print to standard out ("-o-") into the file merged.gff3.

score 1 · Answer 2 · 2012-08-02

Unfortunately, different flavors of GTF make it difficult to make a generic converter. It is possible that you could create a Bio::DB::GFF database directly from your GTF. Bio::DB::GFF (whose BioPerl loaders are called bploadgff.pl, bpfastloadgff.pl and bpbulkloadgff.pl) works with GFF2 data, and GTF looks a lot like GFF2. I haven't tried it, but it wouldn't surprise me if it worked.

It would be best to ask further questions on this topic on the GBrowse mailing list (https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse) since there are lots of people on that list who deal with problems like these on a regular basis.