Question: customProDB: issues getting non-model organism dbsnp
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gravatar for kristenbeck527
3.7 years ago by
United States
kristenbeck52710 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

 

snp customprodb var ensembl • 835 views
ADD COMMENTlink written 3.7 years ago by kristenbeck52710
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