Hi,

I am using qiime2-2019.7.

I would want to know is there any command to know how many sequences are being removed during the different filtering steps in denoising by DADA2.

After demultiplexing, the sequence count for my samples were as follows:

sample-1 - 867483

sample-2 - 425562

sample-4 - 344595

sample-3 - 310675

sample-5 - 288880

sample-6 - 288164

sample-7 - 280172

After that, I have run the following script for denoising:

qiime dada2 denoise-paired --i-demultiplexed-seqs paired-end-demux.qza --p-trunc-len-r 202 --p-trunc-len-f 248 --o-table paired-table.qza --o-representative-sequences rep-seqs-paired.qza --o-denoising-stats denoising-stats-paired.qza --p-chimera-method consensus --verbose

This step has resulted in the following feature count for my samples:

sample-1 - 43215

sample-2 - 13685

sample-6 - 12421

sample-4 - 10195

sample-7 - 9718

sample-5 - 7645

sample-3 - 7617

How do I know How many sequences are filtered during denoising, then merging and chimera removal. This would help me to make sure that not so many sequences are filtered out. Is there any commands to help me?

Looking forward for suggestions.

Thanks

Regards

Femi Thomas