Hi dear developers,
I was wondering for the humann2_unpack_pathways script,
1. Should I use cpm normalized table for both genefamily and pathway abundance table right?
2. How to interpretate the results?
The command i ran is
humann2_unpack_pathways --input-genes humann2_genefamilies_cpm.tsv --input-pathways humann2_pathabundance_cpm.tsv \
--remove-taxonomy --output humann2_pwa_unpacked.tsv
And a sample output table is as attached.
The header row still has all of the sample names, but the following rows generally is the "pathway|genefamily and then some number (I think its cpm)" format.
I was wondering why we can't see each sample's cpm in that corresponding pathway|genefamily?
How is the number calculated from the two input tables?
Thank you very much for your time