i have a list of ensembl_transcript_id_version, and I want to map the ensembl_gene_id and external_gene_name to it. However, it does not find a hit for a lot of genes (e.g. the id: ENSMUST00000109424.2, only if I change the version from .2 to .3).
ensembl <- biomaRt::useMart(biomart = "ENSEMBL_MART_ENSEMBL", host = "www.ensembl.org") mart <- biomaRt::useMart(biomart = "ENSEMBL_MART_ENSEMBL", dataset = "mmusculus_gene_ensembl", host="www.ensembl.org") transcript2gene_test1 <- biomaRt::getBM(attributes = c("ensembl_transcript_id_version", "ensembl_gene_id", "external_gene_name"), filters=c('ensembl_transcript_id_version'), values = c("ENSMUST00000109424.2","ENSMUST00000109424.3") , mart = mart)
Is it possible to find a match for transcripts like ENSMUST00000109424.2, or do I have to remove the version number and just query for ENSMUST00000109424 (Or does this has other downsides.)
Thanks in advance.