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
Lukas