Hi @kla89,
Could you please provide some more information on your data? E.g.,
- what type of library preparation and sequencing methods are you using? (in particular, what type of barcodes, primers, and marker gene are you using?)
- what is the length of your sequences?
- what is the command that you are using?
My guess is that you may have an in-line barcode or some other piece of non-biological sequence present within the sequence reads that is not being trimmed prior to dada2. This would cause each feature to be unique to a single sample. Does that make sense, based on your methods?