build TSS from biomaRt for ChIPpeakAnno, how to decide the mm9 and mm10 assembly?
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Julie Zhu ★ 4.3k
@julie-zhu-3596
Last seen 15 days ago
United States
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 [[alternative HTML version deleted]]
Mus musculus biomaRt ChIPpeakAnno Mus musculus biomaRt ChIPpeakAnno • 2.7k views
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