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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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Taxonomic table for extraction of certain levels #484

Open ts-dangelo opened 9 months ago

ts-dangelo commented 9 months ago

Hi,

I am using eggnog to annotate metagenome assemblies that contain all domains of life. I want to exclude Eukaryotes from my analyses. It seems that there are multiple ways to do this using --tax_scope and --target_taxa options. Other open Issues seem to suggest using these flags can alter the results. I would prefer to annotate the dataset without one of these flags and then filter the dataset using the best_tax_level column in the annotation file. Is there a table of the taxonomic level names used in eggnog that can be made available so that one could write a script to filter large sets of results based on the taxonomic names in that column? Is there another built-in way for me to exclude sequences with Eukaryotic annotations in the best_tax_level column?

Thanks

Cantalapiedra commented 9 months ago

Hi @ts-dangelo ,

You may use the eggNOG_OGs field (a comma separated list of OG@tax_id|tax_name), filtering by tax_id or tax_name. Eukaryota id is 2759.

https://github.com/eggnogdb/eggnog-mapper/wiki/eggNOG-mapper-v2.1.5-to-v2.1.12#orthologous-groups-fields

Best, Carlos