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? Many thanks, Michele [[alternative HTML version deleted]]

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