Question: customProDB: issues getting dbSNP data for non-model organism
0
4.1 years ago by
United States
kristenbeck5270 wrote:

I'm trying to use PrepareAnnotationEnsembl() function in customProDB. Based on Ensembl's site the current dbSNP version for Macaca mulatta is snp131. However, if I try to enter that into the function I get an error.

ensembl = useMart(biomart="ensembl")
ensembl = useMart("ENSEMBL_MART_ENSEMBL", dataset = "mmulatta_gene_ensembl", host="may2012.archive.ensembl.org")
PrepareAnnotationEnsembl(mart=ensembl, annotation_path=annotation_path_mm, splice_matrix = FALSE, dbsnp="snp131", COSMIC=TRUE)

I have also tried just using the number e.g. dbsnp="131". Both commands return the following error:

Error in pmatch(dbsnp, dbsnps) : object 'dbsnps' not found

Without adding the dnsnp parameter, it retrieves the annotation data. Also, in the source of the function, it is set up to query human and mouse dbSNP data. Could it be that non-model organisms aren't supported for dbSNP reference data retrieval? Any help on this would be greatly appreciated.

-Kristen

modified 4.1 years ago by xiaojing.wang50 • written 4.1 years ago by kristenbeck5270
Answer: customProDB: issues getting dbSNP data for non-model organism
1
4.1 years ago by
United States
xiaojing.wang50 wrote:

Thank you for your reply! Do you have any suggestions on converting the Biomart table to the expected Granges format that the subsequent functions are expecting?

1

Hi Kristen,

Try makeGRangesFromDataFrame() from the GenomicRanges package.

H.