Hello, forum,

I want to map the mouse transcript id like ENSMUST00000159265.1 to the human transcript id which starts with "ENST" using the biomaRt, but I failed. What is wrong with my code, or is the idea unrealistic?

My code is as follows:

library("biomaRt")
human <- useMart("ensembl", dataset = "hsapiens_gene_ensembl", host = "https://dec2021.archive.ensembl.org/") 
mouse <- useMart("ensembl", dataset = "mmusculus_gene_ensembl", host = "https://dec2021.archive.ensembl.org/")
# View(listAttributes(mouse))
# View(listAttributes(human))
getLDS(attributes = c("mgi_trans_name"), filters = "mgi_trans_name", 
       values = c("ENSMUST00000159265.1") , mart = mouse, 
       attributesL = c("hgnc_trans_name"), martL = human, 
       uniqueRows=T)
getLDS(attributes = c("mgi_symbol"), filters = "mgi_symbol", 
       values = c("Xkr4") , mart = mouse, 
       attributesL = c("hgnc_symbol"), martL = human, 
       uniqueRows=T)
getLDS(attributes = c("mgi_id"), filters = "mgi_id", 
       values = c("ENSMUST00000159265.1") , mart = mouse, 
       attributesL = c("hgnc_id"), martL = human, 
       uniqueRows=T)

That's an Ensembl transcript ID, not MGI. And you have the wrong version. Here's how you can figure that out.

## just do a simple lookup first, without specifying the version
> getBM("ensembl_transcript_id_version", "ensembl_transcript_id", "ENSMUST00000159265", mouse)
  ensembl_transcript_id_version
1          ENSMUST00000159265.2

## now do the lookup using the correct attributes and filters, with the correct version for that archived database
> getLDS("ensembl_transcript_id_version", "ensembl_transcript_id_version", "ENSMUST00000159265.2", mouse, "ensembl_transcript_id_version", martL = human)
  Transcript.stable.ID.version Transcript.stable.ID.version.1
1         ENSMUST00000159265.2              ENST00000327381.7
2         ENSMUST00000159265.2              ENST00000518261.1
3         ENSMUST00000159265.2              ENST00000622811.1

## or you could be version agnostic, so you don't have to make sure you have the right archive version

> getLDS("ensembl_transcript_id_version", "ensembl_transcript_id", "ENSMUST00000159265", mouse, "ensembl_transcript_id_version", martL = human)
  Transcript.stable.ID.version Transcript.stable.ID.version.1
1         ENSMUST00000159265.2              ENST00000327381.7
2         ENSMUST00000159265.2              ENST00000518261.1
3         ENSMUST00000159265.2              ENST00000622811.1