Question: customProDB: issues getting dbSNP data for non-model organism
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gravatar for kristenbeck527
3.8 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

ADD COMMENTlink modified 3.8 years ago by xiaojing.wang50 • written 3.8 years ago by kristenbeck5270
Answer: customProDB: issues getting dbSNP data for non-model organism
1
gravatar for xiaojing.wang
3.8 years ago by
United States
xiaojing.wang50 wrote:
The function PrepareAnnotationEnsembl() is unable to retrieve dbSNP information for species other than human and mouse. Because we choose to only download the data in coding region through UCSC table browser for performance reason (the dbSNP data is huge and is getting larger and larger). You can use biomaRt to download the dbSNP data or directly download it from ftp://ftp.ensembl.org/pub/release-74/variation/gvf/macaca_mulatta/ Xiaojing From: kristenbeck527 [bioc] [mailto:noreply@bioconductor.org] Sent: Tuesday, July 07, 2015 12:46 PM To: Wang, Xiaojing Subject: [bioc] customProDB: issues getting dbSNP data for non-model organism Activity on a post you are following on support.bioconductor.org<https: support.bioconductor.org=""> User kristenbeck527<https: support.bioconductor.org="" u="" 8349=""/> wrote Question: customProDB: issues getting dbSNP data for non-model organism<https: support.bioconductor.org="" p="" 69592=""/>: 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 ________________________________ Post tags: ensembl, macaque, dbsnp, customprodb You may reply via email or visit customProDB: issues getting dbSNP data for non-model organism
ADD COMMENTlink written 3.8 years ago by xiaojing.wang50

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?

ADD REPLYlink written 3.8 years ago by kristenbeck5270
1

Hi Kristen,

Try makeGRangesFromDataFrame() from the GenomicRanges package.

H.

ADD REPLYlink written 3.8 years ago by Hervé Pagès ♦♦ 13k

Great! Will do. Thank you. 

ADD REPLYlink written 3.8 years ago by kristenbeck5270
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