I'm trying to cleanup my data but there's not enough overlap between forward and reverse samples. I've already increased the retaining area but still not enough overlap in a few samples. What should I do? Is there any code to remove such samples?
This is the error message: /var/folders/sm/q87dz81s50l651tfwfcf2vsc0000gn/T/qiime2-q2cli-err-h38dwv8x.log
Can you send a screenshot of your interactive quality plot?
Dada2 filters out the sequences that don't join so if after dada2 you have no sequences that means that they were all filtered out (possibly because they didn't join possibly for other quality reasons).
If there is no way to make the sequences overlap then you could run dada2 denoise-single and stick to a single end read analysis although I understand that is not preferable
Truncating your reverse reads just before your quality drop off near bp 225 might do the trick, but I am afraid you may end up having to use @cherman2's suggestion of performing a single end analysis.