I'm trying to convert ensembl gene IDs to gene symbols. The ensembl gene IDs come from human reference file: Homo_sapiens.GRCh38.dna.primary_assembly.fa. I've tried using the BioMart tool from ensembl and the BioTools Converter (https://www.biotools.fr/human/ensembl_symbol_converter), but both tools still give me a lot of blank gene symbols (they don't convert from gene ID to gene symbol). Does anyone know of another gene ID converter that I can try that would give me the complete list of gene symbols for this human reference file?
Thank you!
For example, these IDs don't convert using biomart:
ENSG00000284928 ENSG00000284930 ENSG00000284931 ENSG00000284932 ENSG00000284934 ENSG00000284946 ENSG00000284948 ENSG00000284951 ENSG00000284952 ENSG00000284954 ENSG00000284956 ENSG00000284957 ENSG00000284959 ENSG00000284962 ENSG00000284964 ENSG00000284966 ENSG00000284968 ENSG00000284969 ENSG00000284976 ENSG00000284977
Checked a couple.
http://www..ensembl.org/Multi/Search/Results?q=ENSG00000284928;site=ensembl - Novel transcript no official name
http://www.ensembl.org/Multi/Search/Results?q=ENSG00000284930 - uncharacterized so no official gene name
How would you recommend I handle these novel transcripts/uncharacterized ones? How would you do it? Should I use the gene symbols for the ones that convert and leave the ensembl IDs for the novel/uncharacterized ones? That might be a little confusing. Is there any other identifier that I could use for the ones that don't have gene names that would make sense to use?
Thank you
Just to jump in here, Ensembl used to use clone-based names for genes without an official gene symbol. However, since Ensembl 104 we now use the Ensembl stable IDs. More information in the following blog post: https://www.ensembl.info/2021/03/15/retirement-of-clone-based-gene-names/
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This is a frequently asked question with multiple prior threads:
How to use biomart on R to convert Ensembl Gene IDs to Symbols?
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