[BioC] SNP retrieval between two mouse strains

[Hervé Pagès]

Hi Sabrina,

On 03/29/2011 03:08 PM, sabrina wrote:
> Dear list:
> Is there anyway that I can retrieve genome-wide snp differences between
> A/J and C57BL/6J mouse strains, using any of the bioconductor packages?

I don't think Bioconductor has any annotation package containing this
information. Note that Bioconductor does not "produce" annotations, but
re-packages/curates existing ones to make them more convenient to work
with in the Bioconductor environment.

In addition to those re-packaged annotations made available thru
hundreds of annotation packages, Bioconductor also provides several
convenient tools for querying external resources like biomaRt (for
querying Ensembl and other BioMart services), rtracklayer for
downloading tracks from UCSC, and others...

So more importantly than whether or not the information you are looking
for is available thru Bioconductor is the question of whether or not
this information is available somewhere? Do you know any external
resource (Ensembl, UCSC, HapMap, dbSNP, etc...) where this information
can be found?

Note that the C57BL/6J strain is *the* reference genome for Mouse
(latest release is NCBI Build 37, also called mm9 by the UCSC folks).

H.


> Thanks!
>
> Sabrina
>
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-- 
Hervé Pagès

Program in Computational Biology
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