[ensembl-dev] incorporation of dbSNP 132 into ensembl

[Fiona Cunningham]

 Dear Andrea,

I am not sure why you want to do this so it is hard for me to answer
your question but definitely any repetitive region of the genome will
be a candidate for having more than one dbSNP mapping. It is easiest
to go the other way round, i.e. to select all variants have mapping
greater than 1.

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 10 December 2010 21:14, Andrea Edwards <edwardsa at cs.man.ac.uk> wrote:
> Thanks a lot
>
> What about going the opposite way...
>
> what code would you use to find genomic regions that map to more than one
> dbSNP id (or variation feature id).
> It can be any genomic region, just for exploratory purposes.
>
> On 10/12/2010 16:41, Pablo Marin-Garcia wrote:
>>
>>
>> Hello Andrea,
>>
>> I forwarded your question to the ensembl dev mailing list because is
>> better to
>> keep the discussions there. And you will have the chance of being answered
>> by
>> the ensembl-variation people that are the ones with the most up to date
>> knowledge of the API and data.
>>
>> My answer is inlinned:
>>
>> On Fri, 10 Dec 2010, Andrea Edwards wrote:
>>
>>> Hi Pablo
>>>
>>> Sorry to bother you again, I was hoping i could ask you a quick question.
>>>
>>> What happens to dbSNP records that are mapped to multiple locations. Lets
>>> say i had a fictitious record rs100 mapped to chromosome 10 at locui100bp
>>> and 200bp and i had this code
>>>
>>> $slice = $sa->fetch_by_region('chromosome', '10');
>>> foreach $vf (@{$vfa->fetch_all_by_Slice($slice)}) {
>>>
>>> Would i get 2 distinct vf objects for the dbsnp record in this loop; one
>>> at 100bp and one at 200bp and both vf objs would have a map_weight of 2
>>> (ignoring any other complexities)
>>
>> yes you would have the two vf. The concept of 'feature' means something
>> mapped, so if an object  maps several times in the genome it would be stored
>> as several different feature entries (one per mapping).
>>
>> This is way the method used to retrieve the variation-features from a
>> variation has the 'all' in it (fetch_all_by_variation) because this is a
>> 'one to many' relationship.
>>
>>
>>  -Pablo
>>>
>>> thanks a lot
>>>
>>
>>
>> -----
>>
>>  Pablo Marin-Garcia
>>
>>
>>
>
>
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