Trying To Load Reference Genome Annotations Into Chado Database

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11.5 years ago

danielcook2013 ▴ 90

Hello,

I'm trying to devlop a chado + django project. I am trying to load in genome annotations (genes, exons, etc.). I started with this solution below - but that has since dead-ended. The easiest way to load 'feature' data into chado is to use a gff3 file.

http://generic-model-organism-system-database.450254.n5.nabble.com/hg19-gff3-file-td5062180.html

Does anyone know where I can get an hg19 gff3 feature file? Additionally, I would like to associate the Gene Ontology dbxrefs with these features. Any ideas on how I can get to that point?

Thanks, Dan

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ADD COMMENT • link 11.5 years ago by danielcook2013 ▴ 90

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The VAAST distribution has a hg19 gff3 from refseq.

ADD REPLY • link 11.5 years ago by Zev.Kronenberg 12k

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I believe you have already got your gff3 file as you have mentioned here. You might also get hg19 gff3 file from NCBI. You do need both scaffolds and top level gff3. Answer about Gene Ontology is also present in the same gmod thread

ADD REPLY • link 11.5 years ago by Biosidd ▴ 40

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