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
>
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