Yeah, that makes sense and is the way I was doing it with the q2-itsxpress plugin, but standalone ITSxpress only seems to take .fastq files while demux produces a .qza file. If I export the .qza file it gives me all of my samples demultiplexed in .fastq format, but doesn't give just one sequences.fastq file that I can then pass through ITSxpress. Do I have to run it separately for each sample? That doesn't seem right.. what am I missing? Thanks!!