I came across the following information in the Tutorial and wondered if the pathcoverage is still revised and what will be the change.
( Note to instructors: Pathway coverage output is being revised; you may skip reviewing it during tutorials pending these updates.)
To clarify this: We are leaning toward replacing the pathway coverage output file (which is a holdover from the original HUMAnN) with an intermediate abundance file, probably reaction abundances. Modern HUMAnN is tuned such that a non-zero pathway abundance is a good indicator of our confidence in the pathway’s presence, independent of the separate probability estimate provided by the coverage file.
Any updates on this?
This is something we’re changing for the upcoming HUMAnN 4.0.