[Genome] intersection and observed field in dbSNP table

[Brooke Rhead]

Hi Eliot,

Instead of intersecting the SNP table with your custom track, you could 
use the "define regions" function in the table browser.  This tool will 
let you paste or upload up to 1,000 BED-3 or BED-4 formatted regions, 
and the "all fields" or "selected fields" output options will work with it.

If the 1,000-regions limit poses a problem, please let us know.  We can 
help you find a different solution.

Also, since you are working with the refUCSC field in the SNP table, you 
should be aware of a potential "gotcha": the refUCSC sequence for SNPs 
reported on the reverse strand were not reverse-complemented when the 
table was made.  What this means is that, for SNPs on the negative 
strand, the reference allele looks like it does not match either of the 
observed alleles.  Here is an example:

name		strand	refUCSC	observed
rs5983746	-	C	A/G

The refUCSC column is the reference DNA from the positive strand.  So in 
this case, the observed allele on the negative strand would be G, which 
makes more sense when looking at the SNP table.  We plan to correct this 
in all of our SNP tables in the near future.

I hope this information helps.

--
Brooke Rhead
UCSC Genome Bioinformatics Group

We invite you to give us your feedback on the UCSC Genome Browser
through May 31, 2007: http://www.surveymonkey.com/s.asp?U=881163743177



Eliot Bush wrote:
>  hello,
> 
> I want to get all the SNPs which overlap with a custom track I have--but 
> I want the output to include the observed and refUCSC fields. When I use 
> the intersection to do this, the output formats which work (bed, custom 
> track) don't seem to include those fields. Is there any way to do what I 
> want in the table browser?
> 
> thanks,
> Eliot
> 
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