Question: Gff3 Format - Human Genome
6
gravatar for toni
8.9 years ago by
toni2.1k
Lyon
toni2.1k wrote:

Hi all,

Does exist a place where I can easily download a GFF3 file of hg19 human annotations ?

Cheers,

T.

annotation gff format human • 10.0k views
ADD COMMENTlink written 8.9 years ago by toni2.1k
1

Good question. UCSC has always been weirdly hostile to gbrowse: "There is no GFF3 format (yet) for complicated reasons." https://lists.soe.ucsc.edu/pipermail/genome/2009-June/019228.html

ADD REPLYlink modified 11 weeks ago by RamRS25k • written 8.9 years ago by Jeremy Leipzig18k

Ensembl have GTF (which is GFF 2.5 or something). But I want this too.

ADD REPLYlink written 8.9 years ago by Casbon3.2k
9
gravatar for Alex
8.9 years ago by
Alex1.5k
Theodosius Dobzhansky Center for Genome Bioinformatics
Alex1.5k wrote:

Check this url

Data type:
gff3
Build:
hg19
ADD COMMENTlink modified 3 months ago by RamRS25k • written 8.9 years ago by Alex1.5k

That's a really nice link, thanks.

ADD REPLYlink written 8.9 years ago by Gww2.7k

Absolutely, that's a great link. Very helpful ! thank you very much.

ADD REPLYlink written 8.9 years ago by toni2.1k

Is there a spec on what is in and what is out feature wise? There are UTRs which must be inferred by the translation, right?

ADD REPLYlink written 8.9 years ago by Casbon3.2k
1
gravatar for Travis
8.5 years ago by
Travis2.8k
USA
Travis2.8k wrote:

It should be noted that the files linked in the top answer are Ensembl annotations and the chromosome identifiers have NOT been altered to refer to the UCSC hg19 genome.

ADD COMMENTlink written 8.5 years ago by Travis2.8k
0
gravatar for Felix
8.5 years ago by
Felix50
Felix50 wrote:

You can also get all Ensembl data including gene annotation GTFs (which you can convert to GFF3) from here: http://www.ensembl.org/info/data/ftp/index.html.
Through their BioMart you can customize your search and download e.g. a CVS file.

ADD COMMENTlink written 8.5 years ago by Felix50
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