dada2-statistics problem after denoising

Hello everyone! I used dada2 to denoise my paired data. However, when I checked the file dada2_stats.qzv, I found that some samples did not filter. I want to know where went wrong.

I used these code and outputted three files without an error.

time qiime dada2 denoise-paired --i-demultiplexed-seqs paired-end-demux.qza --p-n-threads 15 --p-trunc-len-f 298 --p-trunc-len-r 286 --o-table dada2_table.qza --o-representative-sequences dada2_rep_set.qza --o-denoising-stats dada2_stats.qza

Then I used:

qiime metadata tabulate
--m-input-file dada2_stats.qza
--o-visualization dada2_stats.qzv

Finally, I got the file like the picture.

I tried the denoising step again, and got the same result. :sob:
Can anyone help me with this problem?

MacOS
qiime2-2022.2
anaconda3-2019.7

Hi!
Could you try to decrease --p-trunc-len-f 298 parameter or set it to 0 (disable)?
All reads, that are shorter than truncation parameter are discarded from the analysis at filtering step, so too high value results in severe filtering as in your screenshot.

Best,

2 Likes

Hi,

Thank you for the response! I successfully retained the data according to your method.

Thank you!
M

1 Like