Hello Pengyu,
After selecting your assembly of interest select a gene prediction track
you want to use. You can read more about the gene prediction tracks on
each of their description pages that can be accessed by clicking on the
blue/grey bar to the left of the track in the main browser display or by
clicking on the pulldown menu from the track. Once you have chosen a
gene prediction track go to the table browser
(http://genome.ucsc.edu/cgi-bin/hgTables) and after selecting your
assembly of interest select:
group: Genes and Gene Prediction Tracks
track: (for this example we'll use UCSC genes)
table: knownGene
If you're not sure which tables you want to access, you can also click
on "describe table schema" for any table and it will take you to a
description of that table's contents. To get gene coordinates also select:
output format: "selected fields from primary and related tables"
Once you click on "get output" this will take you to a menu where you
can choose to include name, chrom, txStart/End in the output.
If you want the entire knownGene table (which includes information other
than just the gene coordinates) you can get it from our downloads page
(this example url is for hg19 - see knownGeneMrna.sql):
http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/
Hopefully this information was helpful and answers your question. If you
have further questions or require clarification feel free to contact the
mailing list at [email protected].
Regards,
Pauline Fujita
UCSC Genome Bioinformatics Group
http://genome.ucsc.edu
On 12/01/10 11:29, Pengyu Hong wrote:
> Hi,
>
> Which file should I download to get human gene position annotations?
>
> Thanks,
>
> Pengyu
> _______________________________________________
> Genome maillist - [email protected]
> https://lists.soe.ucsc.edu/mailman/listinfo/genome
_______________________________________________
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