Download condensed gene list

[Helen Li]

Hi!

I'm trying to do a project that's measuring gene density, but I want to get a gene list and it's coordinates without the alternative splice forms. I want essentially a .txt file of all the genes in the human genome but as the "dense" version of the UCSC genes track. How can I do this?

Thanks!

Helen

[Matthew Speir]

Hi Helen,

Thank you for your question about the getting a gene list from the UCSC
Genome Browser. You may be interested in the knownCanonical table for
the UCSC Genes track, which contains roughly one transcript per gene.
You can get this information from the Table Browser using the following
steps:

1. Navigate to the Table Browser, Select your assembly and tracks.
2. Select your assembly and tracks:

clade: Mammal
genome: Human
assembly: Feb. 2009 (GRCh37/hg19)
group: Genes and Gene Predictions Tracks
track: UCSC Genes
table: knownCanonical
output: BED - browser extensible data
output file: enter a file name to save your results to a file, or
leave blank to display results in your browser

3. Click 'get output'.
4. Select the options for your BED file.
5. Click 'get BED'.

For more information on how to use the Table Browser, please refer to
our help pages:
http://genome.ucsc.edu/goldenPath/help/hgTablesHelp.html

I hope this is helpful. If you have any further questions, please reply
to gen...@soe.ucsc.edu. All messages sent to that address are archived
on a publicly-accessible Google Groups forum. If your question includes
sensitive data, you may send it instead to genom...@soe.ucsc.edu.

Matthew Speir
UCSC Genome Bioinformatics Group

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