I am testing my 16S data using DADA2 on 2x250 paired end reads. This was the quality score box plots.
qual_viz.qzv (309.8 KB)
Based on the results, the sequences were denoised with DADA2.
The script i used:
qiime dada2 denoise-paired --i-demultiplexed-seqs 16s_cb_paired-end-demux.qza --o-table table --o-representative-sequences representative_sequences --p-trunc-len-f 240 --p-trunc-len-r 240 --p-trim-left-f 20 --p-trim-left-r 20 --o-denoising-stats denoising-stats.qza
This was the denoising stats
stats.tsv (3.5 KB)
It looks like most of our sequences were dropped out because they fail to merge.
I wonder why so many reads were lost especially for sample A7, M1, and F1.
Thanks in advance.