This is a test version of Biostars. For the public version, visit https://www.biostars.org.
biomaRt GRCh37 down?

Hi,

Using the connection string:

grch37      <- useMart(biomart = "ENSEMBL_MART_ENSEMBL", 
                       host    = "grch37.ensembl.org", 
                       path    = "/biomart/martservice", 
                       dataset = "hsapiens_gene_ensembl")

Doesn't appear to work, with the error:

Extra content at the end of the document
Error: 1: Extra content at the end of the document​

Any idea if this is an error with my code, or is the service down?

Thanks

ensembl biomart
• 3,226 views • link
updated by Ram Ram • written by andrew.j.skelton73 andrew.j.skelton73

1 answer

We're working on it!

• 0 views • link
written by Emily Emily

Should be back now.

• 0 views • link
written by Emily Emily

Log in to answer this question.

More posts like this
  • GATK GRCh38 genome version for biomaRt
    written by ramiro.barrantes • ramiro.barrantes
    Hello, I am using iGenomes GATK.GRCh38 with sarek. Now I need to use the R package biomaRt to fetch the sequence and other information. What …
  • Can´t acces Biomart via R anymore
    written by Beginner • Beginner
    Hi, my R code previously accessed Biomart via: library("biomaRt") mart=useMart(biomart="ENSEMBL_MART_ENSEMBL", dataset="mmusculus_gene_ensembl", host="www.ensembl.org") resMArt=getBM(attributes=c("ensembl_gene_id","description","mgi_symbol"),mart=mart) resMArt2=getBM(attributes=c("ensembl_gene_id","gene_biotype"),mart=mart) however, mart=useMart(biomart="ENSEMBL_MART_ENSEMBL", dataset="mmusculus_gene_ensembl", host="www.ensembl.org") now gives the error: Error in listMarts(host …
  • dbSNP build in ENSEMBL biomaRt?
    written by 09meh • 09meh
    I'm wondering how to determine what dbSNP build (i.e. 150 or 151) the variation annotations are based on. For example, I can find that for …
  • GetBM gives controversial results
    written by lizaveta • lizaveta
    I want to get chromosome location of SMARCA1 gene. library("biomaRt") human = useMart(biomart="ENSEMBL_MART_ENSEMBL", dataset = "hsapiens_gene_ensembl",host="grch37.ensembl.org", path="/biomart/martservice") getBM(attributes = c("hgnc_symbol","chromosome_name", "start_position", "end_position","strand"), filters = "hgnc_symbol", …
  • Ensembl biomaRt down
    written by sergio.artsc • sergio.artsc
    I am trying to get some queries from biomaRt package. I am defining the next connection: snp_db <- useMart("ENSEMBL_MART_SNP", dataset="hsapiens_snp", host="grch37.ensembl.org") and I get the …
  • BioMart: connection fails
    written by salamandra salamandra
    Hi, running this > ensembl = useMart(biomart > ="ENSEMBL_MART_ENSEMBL",dataset="hsapiens_gene_ensembl", host="may2017.archive.ensembl.org") or this: > ensembl = useMart(biomart > ="ENSEMBL_MART_ENSEMBL",dataset="hsapiens_gene_ensembl", host="http://dec2017.archive.ensembl.org") used to work in the past. …
  • using biomaRt in R to annotate SNPs to Genes within 1000kb
    written by Sheila Sheila
    Hi! In short, I have a list of SNPs that I would like to map to the closest gene within 1000kb. I am using the …
  • biomaRt GRCh37 down?
    written by alexander.nash • alexander.nash
    Hi, I am currently getting the following error: library(biomaRt) mart<-useMart(biomart="ENSEMBL_MART_ENSEMBL", dataset="hsapiens_gene_ensembl", host="grch37.ensembl.org") Extra content at the end of the document Error: 1: Extra content at …
  • Map ensembl gene id form hg38 in hg19
    written by Tanvir Ahamed Tanvir Ahamed
    I want to map all ensembl gene id form hg38 in hg19. Any help will be appreciated ? Thanks !! # Example : Loading library …
  • Ensembl biomaRt Down?
    written by andrew.j.skelton73 andrew.j.skelton73
    Hi, Currently getting the following error: library(biomaRt) ensembl <- useMart("ensembl") Extra content at the end of the document Error: 1: Extra content at the end …