[ensembl-dev] Affymetrix Porcine probes: genomic position

[Dario Beraldi]

Hi Laurent,

Thanks for taking time to reply. Unfortunately, the file  
Sus_scrofa.gvf.gz has the probe location for the Illumina Porcine SNP  
chip. What I'm after is the probe location of the Affymetrix Porcine  
gene expression array (this one:  
http://www.affymetrix.com/browse/products.jsp?productId=131488&navMode=34000&navAction=jump&aId=productsNav#1_1).

I had a look into the subdirectories within  
ftp://ftp.ensembl.org/pub/release-62/ I but couldn't find anything  
relevant.

Any ideas...?

All the best
Dario

Quoting Laurent Gil <lgil at ebi.ac.uk> on Tue, 26 Apr 2011 13:27:33 +0100:

> Hi Dario,
>
> You can find all the ensembl data on the ftp:  
> http://www.ensembl.org/info/data/ftp/index.html
>
> The pig variations are stored here:  
> ftp://ftp.ensembl.org/pub/release-62/variation/sus_scrofa/
> The file that might interest you is Sus_scrofa.gvf.gz  
> <ftp://ftp.ensembl.org/pub/release-62/variation/sus_scrofa/Sus_scrofa.gvf.gz>.
>
> Cheers,
>
> Laurent
>
>
> On 25/04/2011 19:23, Dario Beraldi wrote:
>> Hello,
>>
>> I'm working with the Affymetrix Porcine chip (gene expression array  
>> for pig). I would like to download the position where each probe  
>> maps on the pig genome.
>>
>> (I can see this information is present somewhere in ENSEMBL for  
>> example  
>> http://www.ensembl.org/Sus_scrofa/Location/Genome?db=core;fdb=funcgen;ftype=ProbeFeature;g=ENSSSCG00000014369;id=Ssc.4978.1.S1_at;ptype=pset;r=2:129356198-129357848;t=ENSSSCT00000015699 but I can't figure out how to extract the genome position in batch for all the  
>> probes).
>>
>> Many thanks!
>>
>> Dario
>>
>



-- 

Dr. Dario Beraldi
Institute of Evolutionary Biology
University of Edinburgh
West Mains Road
Edinburgh EH9 3JT
Scotland, UK


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