Thanks for your help. For my data, I can observe multiple sequences with at least 90% similarity, and part of thses sequences that quality score only have single nucleotide differences. But I not sure this is main reason.
I was able to take a closer look at your data and it looks like it may not have been collected on an Illumina machine, based on the values of the PHRED scores present. The scores you have in your data contain a wider range of values than would be present in a single Illumina variant on its own, as well as having longer reads than would be expected with the standard Illumina reads. Do you know what technology was used to sequence your data? If not could you ask your sequencing center?
Hi, I try to use the denoise-ccs, but my data have been dealt with, it does not contain front and adapter, so I wonder if the qiime2's development team could consider adjust the parameters' setting. And I also try to ask for the original data, but it has been a little long, the original data may be deleted.
Thanks for your help.
@ZHY I will have to look into that, the denoise-ccs method is a recent addition and I think generally the adapters and primers are still included, but do not see why they would have to be. These are not required parameters for other tools in q2-dada2, so I do not think they need to be required here, but need to check to make sure I am not missing something.