[BioC] How to use cutome reference genome?

[Kasper Daniel Hansen]

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/inst/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.
>
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