For various reasons, I am obligated to analyze RNA and Chip sequencing data with a UCSC reference genome and to annotate with the program ChIPpeakanno. However, I can only get Chippeakanno to work with an ensemble reference generated by ....
mart = useMart(biomart = "ensembl", dataset = "mmusculus_gene_ensembl")
getAnnotation(mart, featureType = "TSS")
UCSC is not available through this method and I have not been able to view this object in order to get the correct UCSC data in the proper format. Any suggestions, other than repeating three weeks of RNA and Chip-seq work with ensemble, would be welcome.