I realized I forgot to add the reverse compliment parameters to my
qiime demux... command. This was an oversight because this time I wasn’t the one who barcoded and prepped these samples so I just didn’t have it on my mind.
I noticed that it runs with no errors, but obviously the code was looking for the wrong sequence so it makes sense I was missing most of my samples and had sequence counts of about 1 or 2. If I hadn’t previously done these analyses, I probably would have really panicked. With sequence counts of below a certain threshold and with so many missing samples, the user could be given a Qiime warning to consider using reverse compliment. Just a thought because I could see this being a stressor for users especially in such an important early step. Just an idea.