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[biomart-users] problems of getting SNPs within a genome range

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[biomart-users] problems of getting SNPs within a genome range

Zhaoming Wu
Dear all,

I'm using biomart to extract some SNPs within a range in the chicken genome.
what I found is when I search the beginning of a chrome even in a large range, the results return in a few seconds, e.g.
> getBM(attributes = c('snp','refsnp_id'),filters = c('chr_name','start','end'),values = list(15,1,20000),mart = gal5_snp)

but when it comes to my regions of interest (15:12291177,12296403)
> getBM(attributes = c('snp','refsnp_id'),filters = c('chr_name','start','end'),values = list(15,12291177,12296403),mart = gal5_snp)

Although it's only a range of 5000 bp, it takes forever and always ends up with an error :
Error in value[[3L]](cond) : 
  Request to BioMart web service failed. Verify if you are still connected to the internet.  Alternatively the BioMart web service is temporarily down.

Any idea how to resolve this issue?

Thank you & best regards,

Zhaoming

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Re: [biomart-users] problems of getting SNPs within a genome range

Thomas Maurel
Dear Zhaoming,


I also get a timeout when using the BiomaRt package. I’ve cced Mike Smith as he might be able to help you further.

Kind Regards,
Thomas
On 18 Apr 2017, at 05:02, Zhaoming Wu <[hidden email]> wrote:

Dear all,

I'm using biomart to extract some SNPs within a range in the chicken genome.
what I found is when I search the beginning of a chrome even in a large range, the results return in a few seconds, e.g.
> getBM(attributes = c('snp','refsnp_id'),filters = c('chr_name','start','end'),values = list(15,1,20000),mart = gal5_snp)

but when it comes to my regions of interest (15:12291177,12296403)
> getBM(attributes = c('snp','refsnp_id'),filters = c('chr_name','start','end'),values = list(15,12291177,12296403),mart = gal5_snp)

Although it's only a range of 5000 bp, it takes forever and always ends up with an error :
Error in value[[3L]](cond) : 
  Request to BioMart web service failed. Verify if you are still connected to the internet.  Alternatively the BioMart web service is temporarily down.

Any idea how to resolve this issue?

Thank you & best regards,

Zhaoming

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Thomas Maurel
Bioinformatician - Ensembl Production Team
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD
United Kingdom

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