Humann regroup with low Original Feature Count

Microbial community profiling HUMAnN
1

I successfully completed Humann until getting gene families. Now I want to regroup Uniref_90 to KO terms. So I did like following:

humann_regroup_table -i sample_1.tsv -g uniref90_ko -o sample_KO.tsv"

I regrouped the samples and it sounds i got a low grouping rate:

Original Feature Count: 106978; Grouped 1+ times: 4569 (4.3%); Grouped 2+ times: 19 (0.0%)

is this low number acceptable?

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2

That mapping rate is a little on the low side, but not to a concerning degree. It depends on the extent to which the UniRef90s detected from your sample have been annotated in UniProt to other functional systems. In my experience with the human gut, functional systems like KOs and ECs are assigned to ~10% of UniRef90s, while Pfams (my preferred category when I want a higher mapping rate) are assigned to ~50% of UniRef90s.

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