[Genome] Affy SNP array tracks not available in Build 36.1 (hg18)

[Heather Trumbower]

Charlotte:

Thanks for your interest.  I'd like to add a bit to Rachel's reply.

What you will find in the SNP Arrays track for hg18 on genome-test
is both the Affy 250K Nsp/250K Sty set (commonly known as 500K), as well 
as the latest Genome-Wide SNP Array 5.0 from Affy (available as a product 
beginning in February I believe).

I moved the Nsp/Sty data from hg17 by looking up the position of the
rsId in dbSNP build 126.  The Genome-Wide data I obtained directly from 
Affymetrix in hg18 coordinates.

The data I have recently received from Illumina are for their new products
HumanHap300v3, HumanHap550v3 and HumanHap650v3.   These were provided in
hg18 coordinates.

Heather Trumbower
UCSC Genome Bioinformatics Group


On Thu, 26 Apr 2007, Rachel Harte wrote:

> Dear Charlotte,
>
> We have the latest Affy SNP Array data for hg18 on our test server.   We
> also have the latest hg18 data from Illumina.  Once the Illumina
> data is added, then our QA team will test the SNP Array track before its
> release to our public servers. So it will be available on the public site
> in the near future.
> Meanwhile you are welcome to view the track on hg18 on our test server:
> http://genome-test.cse.ucsc.edu
>
> Please note that this data and some other data on the test server has not
> yet undergone QA so it could be wrong and could change at a later date.
>
> 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, 26 Apr 2007, Charlotte Schjerling wrote:
>
>> Dear Sir/Madam
>>
>> I would like to know whether the Affymetrix 500K SNP array tracks for
>> Build 36.1 are planned and if so, when they can be expected to be available?
>>
>> I think it is a really nice feature in Build 35 and I do hope it will
>> be part of Build 36.1 soon.
>>
>> Best wishes,
>>
>> Charlotte Schjerling, M.Sc.
>>
>> RH Microarray Center
>> Department for Clinical Biochemistry, KB 4111
>> Rigshospitalet
>> 9 Blegdamsvej
>> DK-2100 Copenhagen
>> Denmark
>> Tlf. +45 3545 4110
>> E-mail: Charlotte at mRNA.dk
>>
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>>
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