Dear Colleagues
I got a sequencing data from a commercial laboratory with very power sequencing quality. It was not possible to process them for DADA2 using paired end protocol. See the attachment od DADA2.
Then I used only forwarded reads and aligned them against gg-13-8-99-515-806-nb-classifier.qza
At then end of the day I got only 99% taxonomy upto Kingdom level. See attachment.
Shall I try something other to get at least some phylogeny information? May be I used incorrect gg reference or the result is because of poor sequencing quality?
Yes, you probably used the wrong reference. Did you use the primers 515f and 806r? If not, you should use the pre-trained full-length 16S classifiers (I am assuming you are targeting 16S), or train your own classifier following the tutorial.
