[BioC] b37 version of BSGenome for Gviz

[Martin Morgan]

On 08/12/2014 12:43 PM, mehaffey wrote:
> Hello,
>
>
>
> I am looking to see if there is a b37 package comparable to the
> BSgenome.Hsapiens.UCSC.hg19 package?  I would like to use the plotTrack
> function of the Gviz package with my bam files but they were aligned using
> b37.  The with and without chr seems to be causing a problem.  I have exome
> and whole genome files so its a lot of resources to have them duplicated.  Is
> there a b37 version package or a conversion workflow/tool?
>
>

maybe

   seqlevelsStyle(BSgenome.Hsapiens.UCSC.hg19) = "NCBI"

does the trick?

Martin

>
> Many thanks,
>
> Michele
>
>
>
> [[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