Hi Vipin,
You can get the gene annotations/predictions using our table browser.
When viewing the assembly, click on "Tables" in the top blue link bar.
On the table browser page:
- make sure group is set to Genes and Gene Prediction tracks
- make sure region is set to 'genome'
- for track, select the table you want to use. For danRer7 there are
four tables containing this type of information.
- select the table (there are several tracks/tables that might fit
your needs)
-- (once you select a table, you can click the "view table schema"
button and view lots of information about the data in that table.)
- since this is a large data set, I would set an output file name,
rather than have it appear in the browser.
- When you've selected what you need, just click "get output" at the
bottom.
Note, since you said you only wanted assembled chromosomes, you may want
to 'create' a filter, like "chrom does match chr*" before getting the
output.
Also, rather than downloading the gene annotations, you could upload
your repeat annotations as a custom track - or use one of the repeat
tracks we already have and do the intersection with the table browser.
If you have any additional questions, please feel free to email us again.
-
Greg
UCSC Genome Browser Group
On 1/27/11 9:54 PM, Vipin Singh wrote:
> Dear Sir,
>
> I want to map the repeats in Zebra fish as genic and intergenic.
> I have the assembled chromosome repeat annotations.
> Where can i get the gene annotations for assembled chromosomes in Zebra
> fish.
>
> Regards,
> Vipin.
>
_______________________________________________
Genome maillist - [email protected]
https://lists.soe.ucsc.edu/mailman/listinfo/genome
