Hello,
Follow these steps to include the tissue table in your filter criteria:
1. Start with track=Spliced Ests and table=intronEst
2. go into filter, check the related table gbCdnaInfo, and click on the
"allow filtering using fields in checked tables" button.
3. many more linked tables will come up in the results, including the
target table you want to filter with, called "tissue". check this table
and click on the same button as in step 2 above.
4. in the table tissue, set so the "name does match brain" and submit.
5. adjust the output format as desired.
6. It is highly recommended to do two things:
1. limit output using the "region" option (by region of interest)
2. use the "output file" option to download the results to a text
file, not the browser screen.
The data (for human) is routed through two very large tables: intronEst
and gbCdnaInfo. When I attempted to do this with the region = entire
genome for human, the browser complained. The intronEst table will
differ in size for the various assemblies, but gbCdnaInfo is huge for all.
If this sounds tedious (because you want data from the entire genome)
another option is to write an SQL query against the public mySQL server
(use the table browser schema information to help you understand and
join the correct tables/fields). Here are some instructions for that option:
http://genome.ucsc.edu/FAQ/FAQdownloads#download29
Please let us know if we can help more,
Jennifer Jackson
UCSC Genome Bioinformatics Group
Vorstman, J.A.S. wrote:
> Hi there,
>
> Does anyone know how to obtain, using the UCSC table browser, Human spliced
> ESTs, but only those that are expressed in the brain? I just can't figure it
> out; in the genome browser I can select to include tissue = brain which seems
> to work fine. Unfortunately, in the table browser I can't find this selection
> option. Perhaps somebody knows the solution to this problem? Many thanks,
> Jacob
>
> J.A.S. Vorstman, MD PhD
>
>
> University Medical Centre Utrecht
> Dept of Psychiatry, A00.241
> Heidelberglaan 100, 3584CX
> The Netherlands
> Phone ( ) 31 88 755 8180
> Fax ( ) 31 88 755 5406
>
> _______________________________________________
> Genome maillist - [email protected]
> http://www.soe.ucsc.edu/mailman/listinfo/genome
>
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