I am attempting to assign taxa to my ITS reads. I, currently, have between ~2,000 and ~11,000 reads (and ~500,000 total) for my samples post-deblur but only one for a single sample is a ‘unique-reads-hit-reference,’ leaving only that sample with reads in the RepSeq output file.
What approach can be taken to use these 500,000 reads that don’t hit reference?
My q2 code used for this was:
qiime deblur denoise-other
–i-demultiplexed-seqs “reads post pair, qc, and name modificiation”
I’ve also been trying to use “qiime feature-classifier classify-consensus-blast” but can’t find which file should be used for “–I-query”