Dear Mehrbod Estaki,
Thank you very much. They are samples of the same areas a couple times over a period of time, I just made the manifest file with appropriate sample labels delineating sampling periods and it seems to be working fine.
My next step is that I was going to follow Analyzing paired end reads in QIIME 2 through the quality filtering step and then move on to de novo chimera checking and then OTU picking using the latest SILVA database (128). I also have to train the classifier correct? Would just use the following plugins? https://docs.qiime2.org/2017.12/plugins/available/vsearch/uchime-denovo/
https://docs.qiime2.org/2017.12/tutorials/feature-classifier/
https://docs.qiime2.org/2017.12/plugins/available/vsearch/cluster-features-de-novo/
Thank you for your time and help,
Sincerely,
David Bradshaw