Does anyone know of a way to get a list of ENSEMBL gene identifiers for all known tRNA encoding genes for a given species?
At the moment, I am interested in generating such lists for human and mouse.
For other types of genes (rRNAs, snoRNAs, etc.) I am able to use biomaRt to find all such genes, for example:
library(biomaRt) ensembl_mart = useMart(biomart="ensembl") biomart = useDataset('hsapiens_gene_ensembl', mart=ensembl_mart) biomart_genes = getBM(attributes=c("ensembl_gene_id", "gene_biotype"), mart=biomart) my_genes$type = biomart_genes$gene_biotype[match(my_genes$ENSEMBL, biomart_genes$ensembl_gene_id)]
...where "my_genes" is some dataframe of genes (e.g. a count table) with an id field called "ENSEMBL"
tRNAs do not have their own gene_biotype grouping, and therefor a separate approach is needed to find them.
I stumbled across Marc's FDB.UCSC.tRNAs database package and was able to figure out how to at least get a list of tRNA genes:
However, I'm not sure how to map from these entries back to my ENSEMBL gene ids.
Anyone know of a better way?