Hi Lakshmi,
You can retrieve this information from the Table Browser, or download
the table directly from our downloads server. To use the Table Browser
(http://genome.ucsc.edu/cgi-bin/hgTables), select a clade, genome, and
assembly of your choice, then set the following:
group: Genes and Gene Prediction Tracks
track: choose a gene prediction track you would like to use (I'll use
'UCSC Genes' for this example)
table: the default table will be the primary table for that track
('knownGene' in this case)
region: genome
identifiers: if you have a list of identifiers, you can upload a file or
paste in here (click 'paste list')
output format: selected fields from primary and related tables
output file: enter a file name to save your results to a file, or leave
blank to display results in the browser
Click 'get output'. On the following page, select the appropriate fields
(name, txStart, txEnd, for example) then click 'get output'.
For more information on how to use the Table Browser, please refer to
our help pages:
http://genome.ucsc.edu/goldenPath/help/hgTablesHelp.html
You can download this table directly from our downloads server. From the
main page, click on 'Downloads' (located on left-side navigation menu).
On the following page, click on 'Human', scroll down to 'Mar. 2006
(hg18), then click on 'Annotation Database'. This will take you here:
http://hgdownload.cse.ucsc.edu/goldenPath/hg18/database/.
Please contact us again at [email protected] if you have any further
questions.
---
Luvina Guruvadoo
UCSC Genome Bioinformatics Group
On 10/12/2011 10:58 AM, Lakshmi Vara Prasad Koneru wrote:
> Dear Mary,
>
> I have a question regarding availability of data in UCSC Genome Browser. Is
> their any downloadable file which has information about genes and its
> transcription start site with genome address?
>
> Thanks,
> Prasad
>
>
> On Wed, Jun 1, 2011 at 9:00 PM, Mary Goldman<[email protected]> wrote:
>
>> Hi Prasad,
>>
>> You can always view the track details page for more information:
>> http://genome.ucsc.edu/cgi-**bin/hgTrackUi?db=hg18&g=**acembly<http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg18&g=acembly>
>> .
>>
>> I hope this information is helpful. Please feel free to contact the mail
>> list again if you require further assistance.
>>
>> Best,
>> Mary
>> ------------------
>> Mary Goldman
>> UCSC Bioinformatics Group
>>
>>
>> On 5/31/11 3:06 PM, Lakshmi Vara Prasad Koneru wrote:
>>
>>> Hello,
>>>
>>> I have a question regarding hg18 annotation file (acembly.txt.gz). The
>>> hg18
>>> annotation file contain gene names with alternative splicing product
>>> names.For example, if I am looking for notiri gene, the annotation file
>>> contains notiri.bApr07,notiri.aApr07-**unspliced. Out of these two gene
>>> product names, which one should I consider as notiri gene? Can you please
>>> provide a web link which describes acembly.txt annotation file?
>>>
>>>
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> https://lists.soe.ucsc.edu/mailman/listinfo/genome
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