How can I get PHRED quality reports after trimming with dada2?

[microbiotaphyto (Isis Silveira)]

Hello everyone!

I was asked to present phred quality reports before and after trimming, but how can I generate a report after trimming with dada2?
I found another topic here with the same issue, but I don't really understand the answer there and the topic is closed. Sorry about that.
Is there a way to see the quality scores after trimming with dada2? If not with dada2, how would I be able to do it?

Thank you

[lizgehret]

Hi @microbiotaphyto,

Thanks for reaching out!

There isn't a way to generate an interactive quality plot post-dada2 - this can only be generated using qiime demux summarize which happens pre-filtering. Based on your filtering options within DADA2 though, you should be able to compare the interactive quality plot from demux summarize with your parameters, since you'll either be filtering out reads at specific bp lengths or below a certain quality score.

If you're looking for some statistics post-dada2, I'd recommend running metadata-tabulate on the dada2-stats output after denoising your data. This will provide you with a table summary and will give you details as to why sequences were filtered out.

Hope this helps!

Cheers