Hi Jing,
The main table of the gene prediction tracks (for example: UCSC Genes,
RefSeq Genes, Ensembl Genes etc.) have the transcription start (the
txStart field) and end position (the txEnd position) information.
You can use the Table Browser ("tables" on the blue bar on the top of
the main page) to grab only the fields you are interested in. Here is a
quick guide to get you started:
Select the clade, genome and assembly that you wish to use. For example,
if you would like to use the default human assembly (currently hg19)
make the following selections: clade: Mammal; genome: Human; assembly:
Feb. 2009 (GRCh37/hg19).
For "group" choose "Genes and Gene Prediction Tracks." Then choose the
gene prediction track you would like to use. The table that
automatically populates will be the primary table for that track and is
the table you should start with. You can click "describe table schema"
to view descriptions of the table columns.
Make these additional selections: region: genome; output format:
selected fields from primary and related tables.
Click "get output". You will be prompted to select the fields you want
displayed before your results are provided. Since you are interested in
transcription start and end positions, I would suggest that you choose
at least the following fields: name, chrom, txStart, txEnd. Click "get
output" to see your results.
For more information about using the Table Browser see "Using the Table
Browser" by scrolling down past the Table Browser form. It provides
brief descriptions of the Table Browser controls. You can also see the
"User's Guide" at http://genome.ucsc.edu/goldenPath/help/hgTablesHelp.html.
Please don't hesitate to contact the mail list again if you have any
further questions.
Katrina Learned
UCSC Genome Bioinformatics Group
Jing Zhang wrote, On 2/24/2010 11:37 AM:
> Hello,
>
> This is Jing from USC Bioinformatics Department. Currently I have one
> problem in finding some data from UCSC Genome Browser. I need the
> information about transcript definition, for example, for each transcript,
> the starting and ending points of each exon for mouse and chicken, and many
> other species. However, from the table, I can not find such information. And
> then I went to the ftp site, and still don't know where such data is
> located. Would you please help me to get such info?
>
> Many thanks in advance.
>
> Best Regards,
>
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