I fetched a complete list of orthologs between two species using OMAdb in R and it seems there are two main ways the output dataframe distinguishes between genes: omaid and canonicalid.
I want to be able to map the results to my RNAseq dataset which is aligned using Ensembl annotation, so I need a way to convert either the OMA-ID or the Canonical-ID to Ensembl gene names.
The OMA website does that if I search the entry with OMAID and click Gene Information, the right output is labeled under "EnsemblGenomes" but of course I cannot do this one by one since I have an entire genome to cover.
I also noticed multiple OMA-IDs could match to the same Canonical-ID, so even though I had minor success converting Canonical-ID to Ensembl names it doesn't seem ideal.
What is the recommended way to convert OMA-ID to Ensembl gene names?
1 answer
Hi, the best option is to use the oma-Enseml crossrefence file from the downloadsection of the Oma Browser: https://omabrowser.org/oma/current/
The direct link of the mapping file is always https://omabrowser.org/All/oma-ensembl.txt.gz
Best wishes
Adrian
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