Question

Gene And Transcript Id Conversion

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11.8 years ago

Davy ▴ 410

Hi All,

So I'm trying to basically get a list of all Entrezgenes and their corresponding gene names, and transcript ids. I've tried biomart ensembl and UCSC genome browser but had no luck with either. Ensembl gives me lots of missing rows of data, and ucsc doesn't appear to offer any entrez ids at all. Anyone know where I could download, or query a table of all entrezgenes?

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ADD COMMENT • link updated 11.8 years ago by Pierre Lindenbaum 161k • written 11.8 years ago by Davy ▴ 410

score 3 · Answer 1 · 2012-06-18

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11.8 years ago

Pierre Lindenbaum 161k

All the information you're looking is available under: ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/

ADD COMMENT • link 11.8 years ago by Pierre Lindenbaum 161k

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Excuse my ignorance, but any suggestions for the best way to deal with these files? I was looking into parsing them with python, but that seems very DIY for something that should be relatively routine.

ADD REPLY • link 11.8 years ago by Davy ▴ 410

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I would use the ASN1 files, convert it to XML using asn2xml ( http://www.ncbi.nlm.nih.gov/IEB/ToolBox/XML/ncbixml.txt ) and parse it with a (python-based) sax parser

ADD REPLY • link 11.8 years ago by Pierre Lindenbaum 161k