Question: What is the difference between GTF AND GFF format
9
gravatar for Y Tb
5.9 years ago by
Y Tb200
USA
Y Tb200 wrote:

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

rna-seq • 28k views
ADD COMMENTlink modified 5.9 years ago by jason160 • written 5.9 years ago by Y Tb200
3

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 18 months ago by RamRS26k • written 5.9 years ago by Istvan Albert ♦♦ 83k
9
gravatar for jason
5.9 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 18 months ago by RamRS26k • written 5.9 years ago by jason160
1

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

ADD REPLYlink modified 18 months ago by RamRS26k • written 5.9 years ago by Giovanni M Dall'Olio26k

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

ADD REPLYlink modified 18 months ago by RamRS26k • written 2.7 years ago by cmdcolin1.3k
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