My seq depth variation after denoising with QIIME2 2022.8 VERSION

Ideas and Suggestions
1

Hi there,

I have done the denoising step with Qiime2 latest version and my stats qzv results showed a vast difference between the non-chimeric read and the denoised read.

see the attached picture
metadata.tsv (11.3 KB)

I really appreciate any suggestions or comments on this

Thanks
Ethendhar

2

Hello and welcome to the forum!

Did you remove primers before the dada2? Most of the primers are degenerative and it may result in high rate of false positives at chimeras detection step in dada2.
If primers are not removed, I would recommend to delete them with q2-cutadapt first.

Best,

3

Hi,
I got demultiplexed sequence from the Illumina service lab. Moreover, I am totally new to this area. As you mentioned that q2-cutadapt which step should be done before demultiplexed step. Even though I tried this step with qiime2 last version it looks good. Is this due to bug issues? or something else.

here is the table from my old run with qiime2
metadata_old.tsv (11.2 KB)

Thanks
Eddie

4

Primers removal should be done before denoising step (Dada2), not before demultiplexing (actually after demultiplexing and before denoising).

I have some difficulties following here - so you tried to remove primers and after it you do not have a lot of chimeras and data looks better?