[ensembl-dev] getting watson snps
Andrea Edwards
edwardsa at cs.man.ac.uk
Mon Dec 13 17:05:35 GMT 2010
Hello
I received an email saying ebi would make wastons snps available as dump
filesin the next release
The dump files would be great but I am also retreiving lots of other
information about the snps with the snps and that might not necessarily
be in your dump file so i think i have to try other options too.
This is what i have tried so far to get the watson snps and not getting
anywhere fast :)
1. Written perl script to download them from ensembl human variation
database. This works but will take over a month to get all the snps at
the rate at which it seems to be running and i imagine you'll block my
ip address if i leave it running :) Plus I can't leave it a month anyway.
2. I've tried to install the human variation database locally but that
also seems to be having problems. It has been installing the allele
table now for 3 days i think. It is running on a very slow machine but
there are far bigger tables than the allele table so i dread to think
how long they will take. I tried to get access to a better machine but i
wasn't give enough hard disk space but perhaps that will solve the
problem! How long should it take to install the human variation database
(roughly) on a 64 bit linux machine with 2 gig of ram and intel xeon @
2.27GHz? Will it take hours or days?
Is there anything else i can try. I do appreciate that the dataset is
vast and these things will be slow? Perhaps the answer is simply a
faster machine to install the local database and I am looking into this.
I have already looked at getting the snps from dbsnp or directly from
source but i need to get information associated with the snps so will
have the same problems i think of retreiving the associated data even if
i got the 'raw snps' by other means
Many thanks
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