[ensembl-dev] getting watson snps

Fiona Cunningham fiona at ebi.ac.uk
Thu Dec 9 16:53:45 GMT 2010


 Dear Andrea,

We will look into producing the dump file of all SNPs in Watson for
the next release which should make your life easier. Biomart is really
best suited to specific queries and so we should provide dump files
where large amounts of information across the entire genome is
required.

Fiona

------------------------------------------------------
Fiona Cunningham
Ensembl Variation Project Leader, EBI
www.ensembl.org
www.lrg-sequence.org
t: 01223 494612 || e: fiona at ebi.ac.uk



On 9 December 2010 13:46, Andrea Edwards <edwardsa at cs.man.ac.uk> wrote:
> Dear all
>
> I've tried downloading watson snps from biomart by a) the whole set and b)
> chromosome by chromosome and i can't get the data. I have tried requesting
> the data by email (no email received) and direct download (download starts
> but at a rate of 1kb per second and times out after about 12 hours/10 mb
> downloaded).
>
> I have written a script to get the watson snps via the perl api but that is
> running and taking hours so I am scared I will get my ip blocked! There are
> 3 million snps and it took an hour to get 3000 i think
>
> I was thinking of getting the human databases directly but i am awaiting a
> new machine and totally out of disk space. Does anyone you know how big the
> human core and variation databases are when installed?
>
> thanks a lot
>
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