Dear QIIME2 experts,
I have a set of 16s data generated from miseq platform with v3v4 regions sequenced. I used dada2 for qc filtering, followed by taxonomy analysis with v3v4 classifier. However, I am having a problem where the sequence taxonomy classification stop at “bacteria” level. Some have ~90% of abundance of this k__Bacteria;;;;;__.
These are animal samples and some of them with as low as 100 reads. Any insight on this phenomenon? Should I use --p-exclude to remove this?
Any comment will be much appreciated. Thanks.