Hi, I am still working on building custom genome in MeDIPS package. I am
following the BSforge. However, it works in Linux system. And I am using R
package under Windows 7. I am wondering if this can be done under windows
system. The answer may be obvious, but it disturbs me for several days.
Thanks very much for your help! 

 

Yan

 

 

 

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/B
SgenomeForge.pdf

 

Kasper

 

On Fri, Aug 31, 2012 at 5:31 AM, Yan He [guest] <guest@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

 


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