Hi All,
We’re analyzing mouse fecal samples using our shotgun data. We specifically want to test whether a specific taxon contributes to a particular functional pathway.
We ran HUMAnN 3.9 with ChocoPhlAn v31 and UniRef90. We have two groups. We ran MaAsLin using MetaPhlAn output and found that the taxon we’re interested in is more abundant in one of the groups. However, HUMAnN is not attributing the pathway to that taxon.
What would be some potential next steps? We’ve been running HUMAnN following the manual. Should we consider re-running HUMAnN with different settings or a subsetted reference database? We’ve done some post-run checks: HUMAnN could assign many gene families (and many pathways) to the family we’re interested in, but it doesn’t have enough evidence to characterize the pathway.
Thanks!
Claire