'select locusLinkId as geneId, refFlat.*
from refFlat inner join refLink
on refFlat.name = refLink.mrnaAcc
;'
I use the above command to get the exon information for a give Gene
ID. But since some Gene IDs are missing as shown in the following
message, I'm wondering how to get the exon information for all the
known Gene IDs.
https://lists.soe.ucsc.edu/pipermail/genome/2009-December/020652.html
On Mon, Nov 30, 2009 at 12:22 PM, Jennifer Jackson <[email protected]> wrote:
> Hello,
>
> There are a few choices: ftp files from Downloads, extract file (table) using
> the Table browser, or output the file (table) using the public mySQL server.
>
> For most gene tracks, the primary table is in genePred format. This includes
> the coordinates of exons and notes the utr and cds regions.
> http://genome.ucsc.edu/FAQ/FAQformat#format9
>
> Downloads:
> The name of a table in the database is the same as a file on the Downloads
> server (with an added .txt.gz for the data and an added .sql for the mySQL
> schema. All database files on the Downloads server are located by following
> the links Downloads -> common name -> genomic assembly version -> annotation
> database directory. http://genome.ucsc.edu/FAQ/FAQdownloads#download1
>
> Table browser:
> Probably the best option. Open the tool, set the controls to the mouse
> assembly of interest, then track group "Gene and Gene Predictions" and then
> the gene track of interest (UCSC Genes or RefSeq or another of your choice).
> Then, leaving the primary table (the genePred table) selected, click on the
> view schema button. The page has three sections - the table/file schema, a
> list of associated tables along with the linking keys, and sample data or the
> track description (same description found by clicking on the track name from
> the Assembly browser graphic page view). With this option, you can link in
> related tables, customize the format of the output, save results back into
> the browser as a custom track, and other functions. Help with examples:
> http://genome.ucsc.edu/goldenPath/help/hgTablesHelp.html
>
> MySQL:
> Instructions -> in the link download29 you had in your original email
> (below). Using the table browser to understand the table names, the schema,
> what linked tables are also a part of the track, and example data can be
> helpful before building a query if it is complex.
>
> Useful tables to link in alternate/gene names or symbols: kgXref, kgAlias
>
> To find out more about the output formats, go into the FAQ section and click
> into "Data file formats".
>
> Hopefully this will get you started,
> Jennifer
>
>
>
>
> ------------------------------------------------
> Jennifer Jackson
> UCSC Genome Bioinformatics Group
>
> ----- "Peng Yu" <[email protected]> wrote:
>
>> From: "Peng Yu" <[email protected]>
>> To: [email protected]
>> Sent: Monday, November 30, 2009 9:04:30 AM GMT -08:00 US/Canada Pacific
>> Subject: [Genome] How to download the exon regions (start and end positions)
>> of all genes? (mouse)
>>
>> http://genome.ucsc.edu/FAQ/FAQdownloads#download29
>> http://genome.ucsc.edu/cgi-bin/hgTables?org=Mouse
>>
>> I feel that I might be able to do the query by sql or tab browser to
>> find the start and end positions of all the exons (mouse). But I'm
>> not
>> sure how to do it. Would you please give me some detailed
>> instructions
>> on this?
>> _______________________________________________
>> Genome maillist - [email protected]
>> https://lists.soe.ucsc.edu/mailman/listinfo/genome
>
_______________________________________________
Genome maillist - [email protected]
https://lists.soe.ucsc.edu/mailman/listinfo/genome
