DADA2 summary only shows sample ID and feature counts

Hi! I'm very new to QIIME2 (2022.8) so apologies if my question is too basic.

I ran DADA2 and used this command for my V3-V4 dataset:

qiime dada2 denoise-paired --i-demultiplexed-seqs reads_qza/reads_trimmed.qza --p-trim-left-f 0 --p-trunc-len-f 253 --p-trim-left-r 0 --p-trunc-len-r 192 --p-max-ee-f 2 --p-max-ee-r 2 --p-n-threads 1 --output-dir dada2_output --verbose

When I checked the summary file, it showed the following:

I should be able to see other info such as "input", "filtered", "denoised" etc, right? How come I'm only seeing sample ID and feature counts?

Hi @Jean0521,

to get the statistic you are looking for you need to add the following option to your denoising command:
'--o-denoising-stats statistic.qza'

Then if you export the statistic.qza content, you will find the file with the statistic you need:
qiime tools export --input-path statistic.qza --output-path STAT

Hope this help

1 Like

Thanks very much for your help, Luca!

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