Hello biobakery help forum,
I have two questions on the pathway RPKs sum from humann3 output files.
I first looked at individual raw pathabundance.tsv for each sample, the sum of RPKs for each pathway does not equal to sum of pathway|species. I also looked at the collapsed pathabundance_cpm.tsv. The result table also had the same issue. I see humann3 code is very straight forward one line with minimum modification we can do so I am not sure what can possibly go wrong here. Please see a screenshot of this issue attached.
I used masslin2 to find significant pathways. I was trying to explain why this pathway is significant and noticed many species were unclassified in specific pathway, infact, after filtering out pathways in more than 10% of sample, all contribution came from unclassified species, … making it hard to explain it from species level simply because they are unclassified. Do you have suggestions on how I should explain pathways from unclassified species?