[BioC] Building custom genome in MeDIPS

[James W. MacDonald]

Hi Yan,

On 9/19/2012 2:48 AM, Yan He wrote:
> 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!

You will need some extra tools, particularly for the 
building/checking/installing step. The canonical source for info is

http://cran.r-project.org/bin/windows/base/rw-FAQ.html#Can-I-install-packages-into-libraries-in-this-version_003f

These days it is really quite easy to get set up, as Duncan Murdoch 
packages everything in a nice little installer.

Best,

Jim



>
>
>
> 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 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
>
>
>
> 	[[alternative HTML version deleted]]
>
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-- 
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099