[BioC] BSgenome.Mmulatta.UCSC

[Martin Morgan]

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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