Hi bioBakery team!
I wanted to ask a question to clarify what is the difference between the output tables in humann3, as I did not find a clear answer in the documentation.
The question specifically is, what is the difference between the pathabundance file, or taking the genefamilies output and remapping it to KO/GO/etc pathways?
Thank you very much for clarification.
Best,
Mate
HUMAnN quantifies gene families as its most granular output. These can then be summed over their individual annotations to get abundances of KOs, ECs, etc. Pathways are slightly different, as we first (internally) figure out the abundance of their component reactions by summing gene abundances (as with KOs/ECs) and then assign an abundance to the pathway based on the abundance of its least-represented reactions. It’s more nuanced than this, but as an example, if a pathway had three reactions with abundances 100, 25, 10, then the pathway abundance would be ~10, reflecting the fact that all reactions have at least that abundnace.