where to find mouse genome GRCm38/mm10 for biomart R

Question

[Alewa]

how can i find and use mouse Genome assembly: GRCm38/mm10 for biomart query in R?

library(biomaRt)
ensemblGRCm38 <- biomaRt::useEnsembl(biomart = 'genes', 
                         dataset = 'mmusculus_gene_ensembl',
                         version = 'GRCm38')

I tried this but gets error

Error: Specified Ensembl version is not available.
Use listEnsemblArchives() to view available versions.

Answer 1

[ATpoint]

You need the Ensembl version, see https://www.ensembl.org/info/website/archives/assembly.html and search for "Mouse". GRCm38 was the genome build until v102. From v103 on it was GRCm39, so using version=102 (or "102", not sure if you need quotes), should do it.

[Alewa]

thank you!

ensembl102 <- useEnsembl(biomart = 'genes', 
                       dataset = 'mmusculus_gene_ensembl',
                       version = 102)