quastion: genomic coordinates

[Mahboobe Akbari]

Hello,

please introduce me how To download genomic coordinates for all 

known genes for species like sheep, cow and chicken from UCSC, Table Browser.

 

  

Sincerely, 

Mahboueh Akbari

[Cath Tyner]

Hello Mahboueh

​,

Thank you for your interest in the UCSC Genome Browser.

You can read about the various genes in each track's description page:

For example, 

- Go the gateway page: 

http://genome.ucsc.edu/cgi-bin/hgGateway

​ 

​- ​

Select your assembly of choice, such as "cow

​" and press the blue "GO" button.

- Click on any of the track names, such as "RefSeq Genes" under the "Genes and Gene Prediction Tracks" category to go to that track's description page:

Track description page for bosTau8's RefSeq Genes:

http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=bosTau8&g=refGene

From the Table Browser, ​(Tools > Table Browser) you can download 

bosTau8's RefSeq Gene

​ whole-genome ​

​

annotations by following the example below:

clade = Mammal

genome = Cow

assembly = whichever version you would like, bosTau8 is the most recent.

group = Genes and Gene Prediction Tracks

track = RefSeq Genes (or whichever track you prefer)

table = refGene 

(or whichever track you prefer)

region = genome

output format: BED - browser extensible data Note: you can choose other options here, such as "sequence."

click "get output"

Create one BED record: ​check the box  "Whole Gene"​

click the "get BED" button

Alternatively, you can also download genomic data directly from our FTP server:

http://hgdownload.soe.ucsc.edu/downloads.html

http://hgdownload.soe.ucsc.edu/downloads.html#cow

If you are new to the UCSC Genome Browser, you might also be interested in some introductory video tutorials about the browser available
from our training page:
http://genome.ucsc.edu/training/index.html
http://www.openhelix.com/ucsc

Please respond to this list if you have further questions!

Thank you again for your inquiry and for using the UCSC Genome Browser. 

​Please send new and follow-up questions to one of our UCSC Genome Browser mailing lists below:

  * Post to the Public Help Forum: E

mail 

gen...@soe.ucsc.edu

​ or search the Public Archives

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 genome...@soe.ucsc.edu 

or search the Mirror Archives​

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​Enjoy,​

Cath
. . .

Cath Tyner

UCSC Genome Browser, Software QA & User Support

UC Santa Cruz Genomics Institute

UCSC Genome Browser

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