Entering edit mode
6 hours ago
saamhasan55
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10
Hello, I have predicted proteins from a newly assembled genome. But when I try to do an ortholog search using orthofinder it does not map to any orthogroup. BUSCO runs fine and shows good completeness. I carried out the orthofinder analysis with proteomes from other species in the same genus. Proteins from all other species map to orthogroups. What could be the reason for orthofinder not finding any hits for my assembled species?
A reason may be that your gene prediction is off. Did you run BUSCO on your predicted proteome? If the gene prediction is ok, then you should see similar scores for the predicted proteome and the genome.
I ran BUSCO on the predicted proteome in protein mode and got >91% completeness. I also removed multiple isoforms from the same gene.
Not enough detail to make a definitive recommendation. Since this should not happen, an educated guess is that you are doing something wrong, like giving Orthofinder a DNA sequence instead of proteins. To manually test whether you have a good collection of proteins, simply submit 20-50 of them to BLASTp and see whether you get expected hits.
I checked the file and it's definitely proteins. I had previously run BUSCO on protein mode on the same file and got >90% completeness. I ran a random sample of a few proteins on BLAST and got results from related species.