[BioC] BSgenome.Mmulatta.UCSC

Martin Morgan mtmorgan at fhcrc.org
Wed Nov 27 20:33:24 CET 2013


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!!
>
> 	[[alternative HTML version deleted]]
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
>


-- 
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109

Location: Arnold Building M1 B861
Phone: (206) 667-2793



More information about the Bioconductor mailing list