Jean0521
(Jean)
April 28, 2023, 2:21pm
1
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?
llenzi
(Luca)
April 28, 2023, 4:12pm
2
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
Luca
1 Like
Jean0521
(Jean)
April 30, 2023, 11:56am
3
Thanks very much for your help, Luca!
system
(system)
Closed
May 31, 2023, 5:57pm
4
This topic was automatically closed 31 days after the last reply. New replies are no longer allowed.