Question: Timeout on getBM() to retrieve snps from locations
gravatar for Corentin
9 months ago by
Corentin430 wrote:

Hi everyone,

I have a list of 150 locations (eg: "10:112834:113150") and I would like to retrieve the variants found in these locations,

This is the command I use to get the variants (fantom_locs contains the list of locations):

snp_db <- useEnsembl(biomart="snp", dataset="hsapiens_snp")

snps_FANTOM <- getBM(attributes = c('refsnp_id'),
                     filters = c('chromosomal_region'), 
                     values = fantom_locs, 
                     mart = snp_db)

It works for a few locations but then I get a timeout error, I can implement a for loop to fetch the snps on one location at a time, but it is very slow and I just wondered if there was a better way to do this.

For example is it worth it to download a local version of the mart ?

timeout getbm() biomart R • 470 views
ADD COMMENTlink modified 9 months ago by Biostar ♦♦ 20 • written 9 months ago by Corentin430
gravatar for Ben_Ensembl
9 months ago by
Ben_Ensembl1.0k wrote:

Hi Corentin,

Since this query is too large for BioMart, I would suggest using the Ensembl REST API Overlap endpoint, restricting the query using the 'feature=variation' parameter:


Best wishes

Ben Ensembl Helpdesk

ADD COMMENTlink written 9 months ago by Ben_Ensembl1.0k

Cheers ! I Just tried it, it was much faster and gave me the same list of rsid.

ADD REPLYlink written 9 months ago by Corentin430
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