Gff3 Format - Human Genome
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13.9 years ago
toni ★ 2.2k

Hi all,

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

Cheers,

T.

human format gff annotation • 13k views
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1
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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

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

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13.9 years ago
Alex ★ 1.5k

Check this url

Data type:
gff3
Build:
hg19
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That's a really nice link, thanks.

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

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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?

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13.4 years ago
Travis ★ 2.8k

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.

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13.5 years ago
Felix ▴ 90

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.

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