Ensemble Service error

Question

[anasjamshed]

I am trying to convert enseml to gene ids:

library(biomaRt)
library(stringr)


# Use biomaRt to map Ensembl IDs to gene names
mart <- useMart("ensembl", dataset = "mmusculus_gene_ensembl")

expression_data <- read.delim("combined_expression.tsv", header = TRUE, sep = "\t")

# Extract Ensembl IDs from the first column
ensembl_ids <- expression_data[,1]  # Assuming the first column contains Ensembl IDs



gene_ids <- str_replace(ensembl_ids,
                        pattern = ".[0-9]+$",
                        replacement = "")

test_annotation <- getBM(attributes = c("ensembl_gene_id", "external_gene_name", "ensembl_transcript_id"),
                         filters = "ensembl_transcript_id",
                         values = gene_ids ,
                         mart = mart)

but its giving following error:

Error: Your query has been redirected to http://status.ensembl.org indicating this Ensembl service is currently unavailable.

[GenoMax]

Ensembl services have overall become less stable over the last few months. You have no option but to wait the downtime out.

[anasjamshed]

do we have other options like use some other server?

[GenoMax]

Download the annotation GTF and parse locally.

[anasjamshed]

how can I do this for mmusculus_gene_ensembl?

[GenoMax]

GTF file for GRCm39: https://ftp.ensembl.org/pub/release-113/gtf/mus_musculus/

You should be able to figure out where to get GRCm38 version if you need that.