After demultiplexing I have reads (files) per sample and some undetermined reads. e.g.,
Since DADA2 uses the information of a single (full?) MiSeq run, I am not sure if I need to import only the reads assigned to samples or do I even import the undetermined reads?
When importing “Casava 1.8 paired-end demultiplexed fastq”, does it import ALL the fastq.gz files in the --input-path dir? If yes, do I need to keep only those files that I plan to import (as per you answer to Q1) in that folder?
qiime tools import