[Genome] RE1 site SNP analysis...

[Rachel Harte]

Hello Jonathan,

Since you have coordinates and strand information, you can upload a custom
track of the RE1 data and then use that to find the intersection of the
SNPs with the RE1 sites using the Table Browser.

To create a custom track, go to the Genome Gatweway page (click on
"Genomes" from our home page). Then click on the "add custom tracks"
button. This button is also found below the Genome Browser image when
viewing a particular assembly. Help for creating custom tracks is here:

http://genome.ucsc.edu/goldenPath/help/customTrack.html

The custom track that you create will be available for querying in the
Table Browser. You can reach this by clicking on the "go to table
browser" buttom on the custom track manager or click on the "Tables" link
on the top blue bar from any of the Browser pages. Then select the genome
and assembly of interest.

Then follow these steps:
1) Select Variation and Repeats as the group and then SNPs as the track.
2) Make sure that genome is selected as the region.
3) Press the create button for intersection and choose Custom Tracks as
the group and select your custom track and press submit.
4) Choose the output format.

You will get a list of positions of SNPs which overlap the RE1 sites.
Please note that it does not give you any information about the RE1
sites with which they overlap. You can also do the query the other way
round (custom track intersected with SNPs) to get the list of RE1 sites
(and positions) that intersect with SNPs.

Additionally, there is a tool called Galaxy at Penn State University:
http://main.g2.bx.psu.edu/
The advantage of this tool is that you can do the type of intersection
above while preserving information from both the custom track and the SNP
data in the output. This tool is built on top of our Table Browser and if
you follow the link to our home page to Galaxy (left blue menu bar) then it
will also be able to display your custom track in its Table Browser interface
- follow the "Get Data" link. Using the "Join" which you find after
clicking on "Operate on Genomic Intervals", you can intersect data from
the two tracks.

I hope that this helps you. Please let us know if you have further questions.

Rachel

 Rachel Harte
UCSC Genome Bioinformatics Group
http://genome.ucsc.edu


On Thu, 29 Mar 2007, JONATHAN COOPER wrote:

> Hi There,
>
>   I'm a student fairly unfamiliar with UCSC. What i need to do is study
> SNP data for RE1 sites within the human genome. RE1 sites are 21bp
>transcription factor sequences - there are around 1300 genomewide & i'd
>like to search each site for variation. Could you possibly suggest a way
>that i might be able to do this quickly & efficiently? I don't really
>want to have to query these individually:0(. Currently i have sequence,
>coordinate, & strand information for each site. If you could help me out
>here i would be really grateful - i don't really have a clue where to
>start...
>
>   Thanks for your time,
>   Jonathan
> _______________________________________________
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