Hi, I am trying to use the MEDIPS package in Bioconductor. The tutorial says that one of the supplied reference genomes must be used. Does anyone know how to produce a custom reference genome in case one's genome of interest is not one that list? I am directed to BSgenome by the same question posted by Kelly V.. However, the BSgenome is based on the Biostrings-based genome data package. What should I do if I have my own sequenced genome sequence and not published yet? Thanks very much for your help! Yan -- output of sessionInfo(): R version 2.15.1 (2012-06-22) Platform: x86_64-pc-mingw32/x64 (64-bit) locale: [1] LC_COLLATE=English_United States.1252 [2] LC_CTYPE=English_United States.1252 [3] LC_MONETARY=English_United States.1252 [4] LC_NUMERIC=C [5] LC_TIME=English_United States.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base -- Sent via the guest posting facility at bioconductor.org.

In the BSgenome package there is a vignette called something like BSforge. It explains how to make a genome package from your own genome. It is pretty easy, but does require a little bit of experience with making an R package. See http://www.bioconductor.org/packages/2.10/bioc/html/BSgenome.html specifically http://www.bioconductor.org/packages/2.10/bioc/vignettes/BSgenome/in st/doc/BSgenomeForge.pdf Kasper On Fri, Aug 31, 2012 at 5:31 AM, Yan He [guest] <guest at="" bioconductor.org=""> wrote: > > Hi, > I am trying to use the MEDIPS package in Bioconductor. The tutorial says that one of the supplied reference genomes must be used. Does anyone know how to produce a custom reference genome in case one's genome of interest is not one that list? I am directed to BSgenome by the same question posted by Kelly V.. However, the BSgenome is based on the Biostrings-based genome data package. What should I do if I have my own sequenced genome sequence and not published yet? > > Thanks very much for your help! > > Yan > > -- output of sessionInfo(): > > R version 2.15.1 (2012-06-22) > Platform: x86_64-pc-mingw32/x64 (64-bit) > > locale: > [1] LC_COLLATE=English_United States.1252 > [2] LC_CTYPE=English_United States.1252 > [3] LC_MONETARY=English_United States.1252 > [4] LC_NUMERIC=C > [5] LC_TIME=English_United States.1252 > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > > -- > Sent via the guest posting facility at bioconductor.org. > > _______________________________________________ > 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