[BioC] Localizing repetitive regions on a chromosome

rcaloger raffaele.calogero at unito.it
Wed Dec 1 11:08:33 CET 2010

  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 
Any suggestion is more than welcome!


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
www:   http://www.bioinformatica.unito.it

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