Holly,

You can find out the current version by using the following two lines of code.
mart1 = useMart(biomart="ensembl")
listDatasets(mart1)

51         mmusculus_gene_ensembl                 Mus musculus genes (GRCm38)       GRCm38

Here is how you obtain mm10 TSS.

mm10 = useMart(biomart="ensembl", datset="mmusculus_gene_ensembl")
TSS.mouse.mm10 = getAnnotation(mart=mm10, featureType="TSS")

For detailed information on how to useMart for different versions or genomes, please type help(useMart) and help(listDatasets).

Please keep the thread in the bioconductor list for others to input/benefit. Thanks!

Best regards,

Julie


On 3/6/13 11:35 AM, "Holly" <xyang2@uchicago.edu> wrote:


Hi, Julie,

 There is a TSS.mouse.NCBIM37 data in the ChIPpeakAnno package.
 I want to use mm10 assembly, and found the tutorial as following. However, it is not clear how to decide the mm9 and mm10 assembly when grabbing TSS from biomaRt. Could you please clarify it? Thanks.
   library(biomaRt)
   ensmart = useMart(biomart="ensembl", dataset="mmusculus_genes_ensembl")
   TSS.mouse.NCBIM37 = getAnnotation(mart=ensmart, featureType="TSS")
   Session <-  sessionInfo()

 Holly





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