[Genome] How to get conservation score from rs number?

[Kayla Smith]

Terry,

Our table browser ("tables" on the blue bar on the top of the web page) is 
useful for intersecting tables.  The instructions are here: 
http://www.genome.ucsc.edu/goldenPath/help/hgTablesHelp.html#Intersection

You'll need to first make a custom track in the table browser out of your 
SNPs.  Then intersect the conservation data with your custom track.

To do this, use the table browser ("tables" link on the blue bar on the 
top of the website)

1.  set the following options:
clade: vertebrate
genome: human
group: Variation and Repeats
track:SNP
table:SNP


2.  identifiers:  paste list of rs numbers and press submit.
3.  output format: custom track
4.  next page, click on "get custom track in table browser".
5.  Go back up to group: and change it to "Comparative Genomics", track: 
Conservation, table: multiz8way.
6.  intersection: click on create. On the intersection page, change group: 
to "Custom Tracks" and select the table you just made.  Click submit.

7.  You're taken back to the table browser page, and now click on "get 
output".


To individually find the conservation score for a snp, type in the rs 
number into the browser position search to center the browser/conservation 
track on your snp.

I hope this helps to answer your question.  If you have any further 
questions please don't hesitate to contact us again.

Kayla Smith


On Thu, 16 Feb 2006, Hsin Terry Shen wrote:

> Could someone please offer some suggestions for how to link the "SNP" table with the  "multiz8way" table?  I need to query the evolutionary conservation scores when I have a list of rs numbers.
>
> Any help would be greatly appreciated!
>
> ~Terry
>
>
>
> _______________________________________________
> Genome maillist  -  Genome at soe.ucsc.edu
> http://www.soe.ucsc.edu/mailman/listinfo/genome
>