Ensembl gene id conversion

Question

[naveedhasan2000]

Hello everyone,

I have a list of ensembl accession ids which i need to convert into the official gene symbols and i used the biomart package and this tool ( https://www.biotools.fr/human/ensembl_symbol_converter ) but some of the ids are not being mapped to any gene symbol, I tried removing version number suffix from the accession ids too but some are still unmapped. How can I map all the ids to corresponding symbols, is there any other utility or way to do it?

[Ben Moore]

Hi naveedhasan2000 - do you have a list of the gene IDs that are not being converted to gene names? The best way to check these is to search in the Ensembl browser to see what's going on: https://www.ensembl.org/index.html

It could be that these genes do not have an official gene symbol, in which case Ensembl reverts to using the gene ID: https://www.ensembl.info/2021/03/15/retirement-of-clone-based-gene-names/

or that the gene IDs come from an older version of Ensembl and have been deprecated, or some other reason.

[naveedhasan2000]

I actually have a list of ensembl ids generated while doing a read count using htseq, i used the reference genome from ensembl. I then tried mapping all these ids to the official gene symbol using biomart and the tool mentioned above but all the ids are not being mapped and its confusing me because these were generated by htseq.

[ATpoint]

Can you add some examples. It is hard to debug textual descriptions.