Hi Lukas, Martin, On 08/14/2013 12:29 PM, Martin Morgan wrote: > On 08/14/2013 12:22 PM, Lukas Chavez wrote: >> Hi Rodrigo, >> >> i) expecting you have the DNA sequence of Eucalyptus grandis, you can >> generate a custom genome by following the instructions you find when >> following he link Marc just sent. > > I'm not sure what purpose the BSgenome package is used for; pointing > Rsamtools::FaFile (perhaps after Rsamtools::indexFa) to your fasta file > might be a sufficient alternative, e.g., method?"getSeq,FaFile" to get > the sequences in regions of interest It looks like some central functions in MEDIPS expect the name of a BSgenome data package as part of the input. But they fail if a BSgenome object or a DNAStringSet object is supplied. Lukas, adding support for this type of input (and maybe also for a FASTA file or FaFile object) should be easy and would make your package much more flexible. Don't hesitate to ask on the Bioc-devel list if you need help with this. Cheers, H. > > Martin > >> >> ii) MEDIPS was not designed for the analysis of MRE-seq. Certainly, >> you can >> easily count the number of mapped reads at genome wide windows, but there >> are no further MRE-seq specific functions available (i.e. MEDIPS does not >> apply any additional constraints that the 5??? end of a read must map >> to the >> CpG site within a methyl-sensitive restriction enzyme site, and no >> MRE-seq >> specific scores are calculated (which are inverse to MeDIP signals as I >> understand?). >> >> All the best, >> Lukas >> >> >> On Wed, Aug 14, 2013 at 11:55 AM, Marc Carlson <mcarlson at="" fhcrc.org=""> >> wrote: >> >>> Hi Rodrigo, >>> >>> Maybe you should have a look at the vignette here? >>> >>> http://www.bioconductor.org/**packages/release/bioc/** >>> vignettes/BSgenome/inst/doc/**BSgenomeForge.pdf<http: www.biocond="" uctor.org="" packages="" release="" bioc="" vignettes="" bsgenome="" inst="" doc="" bsgenomefo="" rge.pdf=""> >>> >>> >>> >>> Marc >>> >>> >>> >>> >>> >>> >>> On 08/13/2013 05:23 PM, Rodrigo Hasbun [guest] wrote: >>> >>>> Hi >>>> >>>> I am a young researcher initiating in the use of short sequences >>>> generated by NGS for methylation analysis. Currently I am working with >>>> MRE-seq in Eucalyptus grandis and I would like to apply MEDIPs for my >>>> analysis . The problem is that I have not a BSgenome for this >>>> species. It >>>> is possible that you generate? >>>> >>>> Best >>>> >>>> Rodrigo >>>> >>>> -- output of sessionInfo(): >>>> >>>> forgeBSgenomeDataPkg("path/to/**my/seed") >>>>> >>>> Error: no se pudo encontrar la funci'on "forgeBSgenomeDataPkg" >>>> >>>>> library(BSgenome) >>>>> >>>> Loading required package: GenomicRanges >>>> Mensajes de aviso perdidos >>>> 1: package 'BSgenome' was built under R version 2.12.1 >>>> 2: package 'GenomicRanges' was built under R version 2.12.1 >>>> >>>>> forgeBSgenomeDataPkg("path/to/**my/seed") >>>>> >>>> Error en .readSeedFile(x, verbose = verbose) : >>>> seed file 'path/to/my/seed' not found >>>> >>>>> forgeBSgenomeDataPkg(/Volumes/**Datos/SeqEuca) >>>>> >>>> Error: inesperado '/' en "forgeBSgenomeDataPkg(/" >>>> >>>>> forgeBSgenomeDataPkg(Volumes/**Datos/SeqEuca) >>>>> >>>> Error en forgeBSgenomeDataPkg(Volumes/**Datos/SeqEuca) : >>>> error in evaluating the argument 'x' in selecting a method for >>>> function 'forgeBSgenomeDataPkg' >>>> >>>>> forgeBSgenomeDataPkg(Volumes/**Datos/SeqEuca) >>>>> >>>> Error en forgeBSgenomeDataPkg(Volumes/**Datos/SeqEuca) : >>>> error in evaluating the argument 'x' in selecting a method for >>>> function 'forgeBSgenomeDataPkg' >>>> -- >>>> Sent via the guest posting facility at bioconductor.org. >>>> >>>> ______________________________**_________________ >>>> Bioconductor mailing list >>>> Bioconductor at r-project.org >>>> https://stat.ethz.ch/mailman/**listinfo/bioconductor<https: stat="" .ethz.ch="" mailman="" listinfo="" bioconductor=""> >>>> >>>> Search the archives: http://news.gmane.org/gmane.** >>>> science.biology.informatics.**conductor<http: news.gmane.org="" gma="" ne.science.biology.informatics.conductor=""> >>>> >>>> >>> >>> ______________________________**_________________ >>> Bioconductor mailing list >>> Bioconductor at r-project.org >>> https://stat.ethz.ch/mailman/**listinfo/bioconductor<https: stat.="" ethz.ch="" mailman="" listinfo="" bioconductor=""> >>> >>> Search the archives: http://news.gmane.org/gmane.** >>> science.biology.informatics.**conductor<http: news.gmane.org="" gman="" e.science.biology.informatics.conductor=""> >>> >>> >> >> [[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 >> > > -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M1-B514 P.O. 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