Hi Martin,

Thanks for the reply!

I get the following:

--------------------------------------------------
> library(AnnotationHub)
> hub = AnnotationHub()
> Mmulatta2 =
hub$ensembl.release.73.fasta.macaca_mulatta.dna.Macaca_mulatta.MMUL_1.73.dna.toplevel.fa.rz
Warning message:
In .getResource(x, name) : incomplete path
> getSeq(Mmulatta2, GRanges("1", IRanges(567089, width=1)))  #A
DNAStringSet instance of length 1
Error in (function (classes, fdef, mtable)  :
  unable to find an inherited method for function ‘getSeq’ for signature
‘"character"’

--------------------------------------------------

Am I doing something wrong, or do I need to install another package?

thanks!


On Wed, Nov 27, 2013 at 2:33 PM, Martin Morgan <mtmorgan@fhcrc.org> wrote:

> On 11/27/2013 08:58 AM, Brian Smith wrote:
>
>> Hi,
>>
>> I wanted to use the Mmulatta genome in bioconductor, but using
>> "available.genomes()", I see that only the rheMac2 (from 2006) is
>> available.
>>
>> UCSC also shows rheMac3 (from 2010). Is there a way that I can
>> download/incorporate this?
>>
>> Essentially, I want to find the nucleotide at specific positions in the
>> rhesus genome (e.g. chr1 - 567089).
>>
>
> Depending on what you're actually interested in,
>
>   library(AnnotationHub)
>   hub = AnnotationHub()
>   Mmulatta = hub$ensembl.release.73.fasta.macaca_mulatta.dna.Macaca_
> mulatta.MMUL_1.73.dna.toplevel.fa.rz
>
> and then
>
> > getSeq(Mmulatta, GRanges("1", IRanges(567089, width=1)))  A DNAStringSet
> instance of length 1
>     width seq                                               names
> [1]     1 G                                                 1
>
> Martin
>
>
>> thanks!!
>>
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>>
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