What is the difference between GTF AND GFF format

Question

[Y Tb]

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

[Istvan Albert]

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

Answer 1

[jason]

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.

[Giovanni M Dall'Olio]

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

[cmdcolin]

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