Hi,
I'm trying out gneiss, and encountered another problem which I would like to ask here.
I used DADA2 to process MiSeq paired end data then analyzed with gneiss, however I found that ASVs belong to the same taxonomic level (genus) are present in both numerator and denominator which is very misleading. So I collapsed the table to genus level first, then at balance-taxonomy step encountered another problem because the featuerIDs are no longer matching, I guess there is way go around it.
I'd like to know if it is more reasonable to work on a taxa collapsed table with gneiss to find out which groups of bacteria really differ?