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eggnogdb / eggnog-mapper

Fast genome-wide functional annotation through orthology assignment
http://eggnog-mapper.embl.de
GNU Affero General Public License v3.0
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about the output #297

Closed Wanli-HE closed 3 years ago

Wanli-HE commented 3 years ago

Hi

i have about 20,000+ genes needs to be annotated, it is nucleotide sequence, so i using the command mode '--itype metagenome'.

and i get the results. but i found only 14,000+ genes are annotated. so my question is, is the result normal? and why are the other 6000+ genes not annotated?

best, wanli

Cantalapiedra commented 3 years ago

Dear @Wanli-HE ,

We have no means to know whether ~70% of genes annotated is normal for your dataset or not. If it is nucleotide sequence, do you mean contigs from an assembly from metagenomics samples? ORFs from MAGs? transcripts? CDS? Do you expect more genes annotated and why?

Best, Carlos

vragh commented 3 years ago

If these are individual nucleotide sequences, you could try translating them (e.g., with TransDecoder and retain only the best ORF for each sequence). If you end up with ca. 14,000 amino acid sequences, that might be one hint at an answer.