Hi Jing,
One of my colleagues just pointed out that you wanted exon start and end
positions rather than transcription start and end positions. Sorry about
that!
Make this change to the selections I originally suggested:
output format: BED - browser extensible data
Click submit. On the page that is displayed, select "Coding Exons" or
"Exons plus [0] bases at each end, whichever is appropriate.
Sorry about any confusion!
Katrina Learned
UCSC Genome Bioinformatics Group
Katrina Learned wrote, On 2/24/2010 2:43 PM:
> 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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