Question: Difference between Ensembl annotation GTF and GFF3 files
2
gravatar for colin.kern
4.3 years ago by
colin.kern660
United States
colin.kern660 wrote:

When downloading the annotation for a genome from Ensembl, there's a GTF and a GFF3 file available. When reading the README files for these two, I'm having trouble determining if these are exactly the same information just in different formats, or if there's a difference in the actual annotations between the two. The wording makes it sound like GFF3 file might include some non-gene features that aren't included in the GTF, and that possibly they have different requirements for evidence to include a gene in each of the files. Does anyone know exactly what the differences are?

annotation ensembl genome • 3.6k views
ADD COMMENTlink written 4.3 years ago by colin.kern660

Did you check this. You will get a primary idea of what these file types contain. 

ADD REPLYlink written 4.3 years ago by venu6.3k

That's describing the differences in the formats, which I'm very familiar with. What I'm asking about is whether the Ensembl genome annotations in the two formats contain the exact same gene and feature sets, or if there's a difference in what is included in each. It's a question about Ensembl's data procedures, not the file formats.

ADD REPLYlink written 4.3 years ago by colin.kern660

Isn't this answerable from downloading relevant pairs of files and comparing?

ADD REPLYlink written 4.3 years ago by Alex Reynolds29k

It's not trivial, but doable, to determine whether they're the same. If they're different, I'm not sure how I'd discern what criteria Ensembl used to generate the two.

ADD REPLYlink written 4.3 years ago by colin.kern660
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