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 [[alternative HTML version deleted]]

Hi, 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 files). 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. HTH, -steve -- 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

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/in st/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]] > > _______________________________________________ > 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 -- James W. MacDonald, M.S. Biostatistician University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099