converting from Ensembl gene ID's to different identifier

Question

I\'ve inherited a dataset of RNAseq output data from Canis Lupus (dog). I have the gene identifier in the Ensembl format, specifically they look like this, ENSCAFT00000001452.3.

Answer 1

Here is step-by-step example:

1. Load the biomaRt library.

   library(biomaRt)
   

2. As query input we have Canis lupus familiaris Ensembl transcript IDs (note that they are not Ensembl gene IDs). We also need to strip the dot+digit(s) from the end, which is used to indicate annotation updates.

   tx <- c("ENSCAFT00000001452.3", "ENSCAFT00000001656.3")
   tx <- gsub("\\.\\d+$", "", tx)
   

3. We now query the database for the Ensembl transcript IDs in tx

   ensembl <- useEnsembl(biomart = "ensembl", dataset = "cfamiliaris_gene_ensembl")
   res <- getBM(
       attributes = c("ensembl_gene_id", "ensembl_transcript_id", "external_gene_name", "description"),
       filters = "ensembl_transcript_id",
       values = tx,
       mart = ensembl)
   res
   #ensembl_gene_id ensembl_transcript_id external_gene_name
   #1 ENSCAFG00000000934    ENSCAFT00000001452            COL14A1
   #2 ENSCAFG00000001086    ENSCAFT00000001656                MYC
   #                                                                   description
   #1               collagen type XIV alpha 1 chain [Source:VGNC Symbol;Acc:VGNC:51768]
   #2 MYC proto-oncogene, bHLH transcription factor [Source:VGNC Symbol;Acc:VGNC:43527]
   

Note that you can get a data.frame of all attributes for a particular mart with listAttributes(ensembl).

Additionally to the link @GordonShumway gives in the comment above, another good (and succinct) summary/introduction to biomaRt can be found on the Ensembl websites.