while I'm struggling to do beta diversity, I found that there is a problem on my table after denoise with DADA2. I double checked my manifest file and metadata file, I reassure that there are 9samples in total in both of them with exact information and file path. But after denoise-single, 3 of them are gone. Only 6 samples remain in table after dada2 denoise and 3 are gone. Below is my code for denoise.
qiime dada2 denoise-single --i-demultiplexed-seqs demux.qza --p-trim-left 0 --p-trunc-len 550 --o-representative-sequences rep-seqs-dada2.qza --o-table table-dada2.qza --o-denoising-stats stats-dada2.qza --verbose
I need help :( thank you