[BioC] Building custom genome in MeDIPS

Steve Lianoglou mailinglist.honeypot at gmail.com
Wed Sep 19 16:11:44 CEST 2012


On Wed, Sep 19, 2012 at 2:48 AM, Yan He <yanhe83 at hotmail.com> 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!

I don't know the answer to the question (I suspect that building the
BSgenome should work, though, once you have all of the appropriate

Section 3.5 of the BSgenomeForge.pdf give you an example that you can
step through to build your own BSgenome. Have you tried getting this
to work on your machine first?

I think it'd be easier to build your custom genome if you first try to
build a "vanilla" one -- this way you will be confident that your
machine can at least do it ... I suspect this will then make you more
productive when building your custom one.


Steve Lianoglou
Graduate Student: Computational Systems Biology
 | Memorial Sloan-Kettering Cancer Center
 | Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact

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