Hi, I'm trying to work out what exactly is happening with my workflow. Hopefully, someone can give me some advice to ID what is happening.
I have samples that were run through QIIME2 and produced a Feature Table and Taxonomy (using SILVA 138.1) that did not identify any Archaea (I was expecting a few but none were identified).
I used the files produced using QIIME2 to create a Phyloseq object and cleaned up the data (orphan ASVs, singletons and doubletons).
I extracted the tables from the filtered Phyloseq object and used them as input for PICRUSt. When I checked the inferred MetaCyc pathways (path_abun_unstrat_descrip.tsv) against the MetaCyc database - I had a number of paths that were identified as specific to Archaea.
Does anyone know why this is happening and if there is any way to identify which ASVs were mapped to these Archeal-specific pathways?
Cheers
Rachele