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

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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.

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written 3.6 years ago by GenoMax

yes! GenoMax @barslmn

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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

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