Thank you very much for your reply!
i have checked with my sequencer center, the sequences had not been quality controlled or filtered.
I plan to denoise it using the following parameters:
qiime dada2 denoise-paired
--i-demultiplexed-seqs paired-end-demux.qza
--p-trim-left-f 0
--p-trim-left-r 0
--p-trunc-len-f 183
--p-trunc-len-r 0
--o-table table_dada2.qza
--o-representative-sequences rep-seqs_dada2.qza
--o-denoising-stats stats_dada2.qza
or
qiime dada2 denoise-paired
--i-demultiplexed-seqs paired-end-demux.qza
--p-trim-left-f 0
--p-trim-left-r 0
--p-trunc-len-f 0
--p-trunc-len-r 0
--p-trunc-q 20
--o-table table_dada2-2.qza
--o-representative-sequences rep-seqs_dada2-2.qza
--o-denoising-stats stats_dada2-2.qza
May I know are the parameters I chose are good to go?
Besides, I've come across a forum that discussed about the similar issue as I am facing now and It was recommended to enforce monotonicity in the fitted error model by changing the error model matrix. May I know is this a necessary step?
Thank you in advance!