chromosome start & end for genes in biomart R not showing

I have a list of genes which i want to get their cordinates and ref-seq ids but "start" & "end" attributes in biomart keeps throwing error. could you please take a look?

library(biomart)
#define which database to use
ensembl102 <- useEnsembl(biomart = 'genes', 
                       dataset = 'mmusculus_gene_ensembl',
                       version = 102)

#define gene ids to query 
ids <- c("ENSMUSG00000047180", "ENSMUSG00000025964", "ENSMUSG00000012187", "ENSMUSG00000055980", "ENSMUSG00000034220",
"ENSMUSG00000026463","ENSMUSG00000026688", "ENSMUSG00000015090", "ENSMUSG00000026879", "ENSMUSG00000027254")

#run annotations
gene_annotations <- getBM(filters = "ensembl_gene_id",
               attributes = c("chromosome_name", "start", "end", "mgi_symbol"),
               values = ids, 
               mart = ensembl102)
Error in getBM(filters = "ensembl_gene_id", attributes = c("chromosome_name",  : 
  Invalid attribute(s): start, end 
Please use the function 'listAttributes' to get valid attribute names

ensembl bioconductor biomart

• 2,132 views • link

updated 3.6 years ago by Ram

• written 3.6 years ago by Alewa

There is a very useful document here that goes over your example too. https://bioconductor.org/packages/release/bioc/vignettes/biomaRt/inst/doc/accessing_ensembl.html

Also, current Ensembl release is 108 if you don't have a specific reason you should stick with the latest release.

• 0 views • link

written 3.6 years ago by barslmn •

Looks like OP wants to use GRCm38 based on the other question so using the latest release would force them to use GRCm39.

• 0 views • link

written 3.6 years ago by GenoMax

yes! GenoMax @barslmn

• 0 views • link

written 3.6 years ago by Alewa

1 answer

Invalid attribute(s): start, end 
Please use the function 'listAttributes' to get valid attribute names

That error message is on the point and even provides you with the solution! You are requesting start and end, but both don't exist. Use

listAttributes(ensembl102)

to list all available annotations.

• 0 views • link

updated 3.6 years ago by Ram

• written 3.6 years ago by Matthias Zepper

Yay! I got it. it was labelled as "start_position" & "end_position" in listAttributes(ensembl102). Thank you!

• 0 views • link

written 3.6 years ago by Alewa

More posts like this

gene symbol not showing for ensembl gene ids using biomart
written 3.6 years ago by Alewa

I have a list of esembl gene ids from RNA-seq experiment and i want to get their corresponding ref-seq ids and gene symbols but the …
gene ID RNAseq
written 4.5 years ago by Rob •

Hi friends How can I get gene numeric ID and hugo ID by R script? what script should I use? I have this but does …
biomaRt: Timeout on getBM().
written 5.1 years ago by lincaijin1994 •

Hi. I want to get the exon annotation of a list of chromosome interval (hg19). Here is the code: getBM_value <- list( chromosome_name = bed_df$chromosome_name, …
gene ensemble ID- no symbol
written 5.4 years ago by Rob •

Hello friends, I used this code to convert ensemble gene ID to gene symbol: df <- read.csv("gene_Ens_ID.csv") library('biomaRt') mart <- useDataset("hsapiens_gene_ensembl", useMart("ensembl")) attributeNames <- c('ensembl_gene_id','external_gene_name','description','gene_biotype', …
GetBM gives controversial results
written 7.9 years ago by 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", …
Xenopus tropicalis Ensembl Gene IDs and Transcripts ID with BiomaRt
written 9.3 years ago by gaby_santos •

Hi! I am trying to retrieve all ensembl gene and transcripts IDs of Xenopus tropicalis using the biomaRt library. getBM(attributes = c('ensembl_transcript_id', 'ensembl_gene_id'), filters ="chromosome_name", …
Ensembl Biomart Plant database
written 9.3 years ago by ####

I want to fetch Arabidospsis annotation via ensembl biomart R package, here is the example how I am trying to fetch it: library("biomaRt") species = …
biomaRt LPR region to position giving different results than I expect (using R)
written 10.8 years ago by Niek De Klein

I am trying to map some ensembl gene IDs and LRG regions to position on the genome. I got the gene IDs and LRG regions …
BiomaRT, retrieve exon positions but filter to chrosomal region
written 11.4 years ago by tonja.r

I am using biomart to retrieve gene/transcripts/exon information and I need exon start and end positions BUT before I need to filter according to the …
How Do I Use Biomart To Get Upstream Flanking Sequence For A Gene?
written 13.9 years ago by Arturo_M •

<p>Hi. I'm trying to get the 100bp upstream sequences of some genes from A. gambiae. I'm using biomaRt and my query looks like this:</p> <pre><code>vector<-useMart("vectorbase_mart_13",dataset="agambiae_eg_gene") …