Mapping ortholog human and mouse transcript

Question

[1769mkc]

For ensmebl ID the mapping can be done which i have tried in biomart, but can the same be done with human transcript id to its mouse and rat counter part ? using biomart or there is/are other ways

UPDATE

human <- useMart('ensembl', dataset = 'hsapiens_gene_ensembl')

getLDS("ensembl_transcript_id_version", "ensembl_transcript_id", "ENSMUST00000159265", mouse, "ensembl_transcript_id_version", martL = human)
Error: biomaRt has encountered an unexpected server error.
Consider trying one of the Ensembl mirrors (for more details look at ?useEnsembl)

[manaswwm]

I usually perform biomaRt queries with their getBM() function where I list the input using filter and values option and my request in the attributes option. Optionally, you could also directly upload your list of gene/transcript IDs and request for the orthologs using the "online" version of biomart hosted here - https://www.ensembl.org/biomart/martview. For example, here is what I queried for getting the ortholog of a human gene's transcript ID - https://www.ensembl.org/biomart/martview/f770c66b31d23f4441e77a7f63bb9a08

As for your error, it seems the server that you are requesting to has a problem. As the error message says, try to change the mirror to someplace else in the useMart function by using the option mirror

Answer 1

[BioinfGuru]

That error is on the server side, nothing to do with you, and is very common. Usually the fix is to try again in an hour, or to insert host = "www.ensembl.org" in the command. So...

human <- useMart('ensembl', dataset = 'hsapiens_gene_ensembl', host = "www.ensembl.org")

Also, maybe you will find the mapping solution you require in these posts:

1. Converting gene ids between 2 species
2. Converting HGNC gene symbols between 2 species

[1769mkc]

for hgnc and ensembl that can be done for transcript id for human to mouse ortholog its difficult to parse and map the exact version from gtf file ,which im trying to for transcript id which is not working