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where to find mouse genome GRCm38/mm10 for biomart R

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.
ensembl bioconductor mouse biomart
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updated by j.gleixner • j.gleixner • written by Alewa Alewa

1 answer

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.

• 0 views • link
written by ATpoint ATpoint

thank you!

ensembl102 <- useEnsembl(biomart = 'genes', 
                       dataset = 'mmusculus_gene_ensembl',
                       version = 102)
• 0 views • link
written by Alewa Alewa

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