Converting Ensemble Gene IDs from mmseq output file

Question

[Dataminer]

Hi,

First of all I know there are various tools already available and discussed here on biostar to convert gene IDs, but the problem I am disvcussing here is bit different.

I have processed my RNA-seq data using mmseq software using ensemble annotation build 70 (link to software is mmseq).

Now I get a list of Ensemble gene IDs and I would like to convert them to gene symbols, the TOTAL number of Ensemble geneIDs that I get is 56625 and upon using biomart ID conversion I am unable to convert all of these into gene symbols.

Does anybody who has used or not mmseq, also encountred a similar problem? If yes how did you fix it?

Note: Species--Homo sapiens

Thank you

Answer 1

[Bert Overduin]

First, as you use annotation from Ensembl version 70, you also should use BioMart version 70 for your Ensembl gene ID to gene symbol conversion. Afaik, the Ensembl BioMart on the Central BioMart server points to the current Ensembl BioMart, which is version 75 (or version 76, in case they already have updated to the brand-new Ensembl release that went live yesterday).

Second, not all Ensembl genes have an HGNC gene symbol assigned (yet), so you will always be missing some.