Great! The untrimmed.qza file has significantly less sequences. And the rest of the sequence almost impossible to match up with my barcode list file. Thankyou very much!
There's a another question I hope you'll answer. It's can be a strange question. What should I do when I run dada2 without denoising but only generating representative sequences and feature tables? And what should I do when I run dada2 denoising without cutting any sequence.
The command I refer as follows:
qiime dada2 denoise-single
--i-demultiplexed-seqs demux.qza
--p-trim-left 0
--p-trunc-len 120
--o-representative-sequences rep-seqs-dada2.qza
--o-table table-dada2.qza
--o-denoising-stats stats-dada2.qza
Thanks again for your professonal knowledge and reponse!
I just read your other post and am following up here.
(Thanks for making a new topic!)
Dada2 always includes denoising. You can change some settings to change how denoising is performed, however. Q2-DADA2 settings
Setting --p-trim-left 0 and --p-trunc-len to the length of your sequence will prevent trimming. The default value for --p-trunc-q is extremely low, but you could also set that to zero if you wanted.
If you want to keep all your reads (so, not trimming and also not removing any reads) also pass
a high value for --p-max-ee
It's only strange because we do not yet know your goal! What biological question are you investigating?