Hi,
I have a question about how HUMAnN outputs its results.
For each EC/pathway, the output includes a row for the total (relative) abundance of the feature in the community per sample, along with rows showing the contribution of different SGBs to that feature.
However, I’ve noticed that the number of taxa contributing to each feature varies. Many taxa have a value of zero in most samples.
My question is:
Is the output filtered to include only SGBs that have at least one non-zero value across all samples in the run?
What exactly is the filtering process HUMAnN uses for reporting SGB-level contributions?
Thanks!