Dear Federico,

Yes. You can ChIPpeakAnno to annotate your peaks with refseq genes/transcripts. You could also use any custom annotation file you have.

One option for obtaining the refseq genes/transcripts would be using GenomicFeatures package. I am ccing Bioconductor listserv for others to chime in.

library(GenomicFeatures)
supportedUCSCtables()

Best regards,

Julie


On 3/29/12 3:58 AM, "Federico Marini" <f.marini@imb-mainz.de> wrote:

 Dear Prof. Zhu,

 My name is Federico Marini, and I started recently my activity as PhD student at the Institute of Molecular Biology in Mainz, Germany.

 I contact you to request additional information regarding one of your published works, namely "ChIPpeakAnno: a Bioconductor package to annotate ChIP-seq and ChIP-chip data", which I had the pleasure to read in detail. I would like to get perform the annotation referring to the refseq genes/transcripts, instead of the ensembl ones. Could it be possible to obtain a similar object for this, and if so, what could be the best/smartest way to do it?

 Since it could be a very precious resource for the needs of our lab, this is why I chose to contact you directly.

 Thanks in advance for your time and attention.

 Best regards,

 Federico Marini



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