What is the difference between GTF AND GFF format

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

rna-seq

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updated 12.3 years ago by jason

• written 12.3 years ago by Y Tb

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

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updated 7.9 years ago by Ram

• written 12.3 years ago by Istvan Albert

1 answer

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.

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updated 7.9 years ago by Ram

• written 12.3 years ago by jason

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

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updated 7.9 years ago by Ram

• written 12.3 years ago by Giovanni M Dall'Olio

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

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updated 7.9 years ago by Ram

• written 9.1 years ago by cmdcolin

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