Hello I have ran qiime picrust2 custom-tree-pipeline on my data using --p-hsp-method mp
My question is related to the pathway abundance and coverage tables. The coverage and abundance of each MetaCyc pathway is calculated how? It reports abundance and coverage over the whole community (predicted metegenome for each sample)? is it corrected by each predicted genome? if so, how? how does it takes into account the number of reactions in each pathway?
I got this from the FAQ section in Picrust2 wiki, however I find it a bit confusing. I don get what “the group being assessed” stands for.
“The coverage is based on the harmonic mean of confidence scores for each reaction in a pathway. The scores will differ depending on what the median reaction abundance is for the group being assessed (i.e. different reaction scores will be inferred if the reaction is within one predicted genome compared to across an entire sample). Since the median reaction abundance will be higher across an entire sample it’s harder to be confident in rare reactions within a sample based on this approach.”
Thanks very much in advance for any help.