Question: What is the difference between GTF AND GFF format
7
gravatar for Y Tb
5.5 years ago by
Y Tb170
USA
Y Tb170 wrote:

What is the difference between GTF AND GFF annotation format and which one should I use to run TopHat

rna-seq • 27k views
ADD COMMENTlink modified 5.5 years ago by jason160 • written 5.5 years ago by Y Tb170
2

To muddy the water even more there is a GFF version 2 and a GFF version 3 format. The evolution was something like this:

GFF 2 -> GTF -> GFF 3
ADD REPLYlink modified 13 months ago by RamRS24k • written 5.5 years ago by Istvan Albert ♦♦ 81k
9
gravatar for jason
5.5 years ago by
jason160
United States
jason160 wrote:

I think it is explained here pretty well.

GTF is a specific instance of the GFF version 2 format.

A flavor of GTF that they are calling 2.2 includes specific 9th column terms transcript_id, protein_id, gene_id

My experience has been GTF 2.2 version works well with TopHat.

ADD COMMENTlink modified 13 months ago by RamRS24k • written 5.5 years ago by jason160
1

It's also well explained in the UCSC FAQs page (see GFF and GTF).

ADD REPLYlink modified 13 months ago by RamRS24k • written 5.5 years ago by Giovanni M Dall'Olio26k

The second link had weird formatting, here is the correct one for "2.2"

ADD REPLYlink modified 13 months ago by RamRS24k • written 2.3 years ago by cmdcolin1.2k
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