Dear All, I have a chip-seq experiment and I need to know if my peaks cluster near repetitive regions in the mouse genome. I had a look to the filters available in biomaRt but I could not find any specific filter to retrieve information on the localization of repetitive regions. Does anybody have any suggestion how to localize repetitive regions in a genome based on rtracklayer, biomaRt or any other tool? I also had the idea of see if my peaks cluster near masked regions in the BSgenome.Mmusculus.UCSC.mm9 but I do not know if is a good or stupid idea. Any suggestion is more than welcome! Cheers Raffaele -- ---------------------------------------- Prof. Raffaele A. Calogero Bioinformatics and Genomics Unit MBC Centro di Biotecnologie Molecolari Via Nizza 52, Torino 10126 tel. ++39 0116706457 Fax ++39 0116706487 Mobile ++39 3333827080 email: raffaele.calogero at unito.it raffaele[dot]calogero[at]gmail[dot]com www: http://www.bioinformatica.unito.it

On Wed, Dec 1, 2010 at 2:08 AM, rcaloger <raffaele.calogero@unito.it> wrote: > Dear All, > I have a chip-seq experiment and I need to know if my peaks cluster near > repetitive regions in the mouse genome. > I had a look to the filters available in biomaRt but I could not find any > specific filter to retrieve information on the localization of repetitive > regions. > Does anybody have any suggestion how to localize repetitive regions in a > genome based on rtracklayer, biomaRt or any other tool? > You can download the repeat masker table from UCSC using rtracklayer. The table is called "rmsk". > I also had the idea of see if my peaks cluster near masked regions in the > BSgenome.Mmusculus.UCSC.mm9 but I do not know if is a good or stupid idea. > Any suggestion is more than welcome! > Cheers > Raffaele > > -- > > ---------------------------------------- > Prof. Raffaele A. Calogero > Bioinformatics and Genomics Unit > MBC Centro di Biotecnologie Molecolari > Via Nizza 52, Torino 10126 > tel. ++39 0116706457 > Fax ++39 0116706487 > Mobile ++39 3333827080 > email: raffaele.calogero@unito.it > raffaele[dot]calogero[at]gmail[dot]com > www: http://www.bioinformatica.unito.it > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]