DADA2 Denoising Stats - "Denoising" does not remove any sequences

Hello everyone,

I have used dada2 denoise-paired to process my data. The quality of my reads was quite high, which is why I decided not to truncate/trim any reads. I’m 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 0
–p-trunc-len-r 0
–output-dir dada2
–o-representative-sequences representative-sequences.qza
–o-denoising-stats stats.qza

Looking at my denoising stats table, I don’t see any reduction from
“filtered” to “denoised”.

These are the average relative number of sequences retained with each step, compared to the input:

Input: 100%
Filtered: 79.33%
Denoised: 79.33% <- no reduction
Merged: 77.09%
Non-Chimeric: 75.23%

Why is there no reduction from “filtered” to “denoised”? Is it because of the parameters I used?
In layman’s terms, what is happening during the denoising step?

Best wishes

Hi Lukas,
Version 1.6 of the dada2 R package (used in the plugin) corrects all sequences by default. Hence no sequences are lost during denoising.

FYI: Tunable correction was added in the newest dada2 release (1.8) but won’t be available in the plugin until until it moves to the 1.8 dada2 R package.


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