Regarding a command for finding the no.of sequences being removed at each step in denoising.

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.

Femi Thomas

Hi @Femi_Thomas,

Have you looked at your denoising-stats-paired.qza file? You can use qiime metadata summarize to get a visualization, and it should have all the information you’re looking for.


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Thank you so much Justine. I had not checked my denoising-stats-paired.qza file.

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