I’ve been using HUMAnN 3.8.
I got many unclassified results because I think the taxonomic resolution of genus is too precise.
So, I’m interested in obtaining taxonomic results at the order level rather than at the genus level.
Unfortunately it seems that is not possible? Can you please help me ?
I’m not sure whether you can specify the taxonomic level in the HUMAnN directly. Nevertheless, you can ran MetaPhlAn separately and specify the level there:
--tax_lev 'o' (orders only)
Then you can ran HUMAnN and refer to the MetaPhlAn output:
humann_infer_taxonomy -l Genus -d uniref90-tol-lca -i humann_genefamilies.tsv -o Genus/humann_genefamilies.tsv"
It works but I don’t know why there are some stange things like this below.
Why do I have “unclassified” instead of “g__Prevotella” and “g__Prevotellaceae_unclassified” in the Genus file?