Not getting anything from the .qzv file

[MANoman (Noman)]

I am not getting any sequence info from the demultiplexed .qzv files.

Any Idea what is the possible error?

[colinbrislawn (Colin J Brislawn)]

Welcome to the forums, Noman!

@MANoman

I am not getting any sequence info

That table is interactive! If you mouse over the plot, the table will automatically update with statistics from that position in the read.

Let us know if you have more questions!

[MANoman (Noman)]

Thanks, Colin! Yes, that's the issue. It shows the same quality score for all the sequence base positions, which feels like all the sequences are the same. I am not sure if there is anything wrong with the data formatting. I have uploaded a picture of how the data is formatted. I am also adding the .qzv file for your reference if you can suggest anything. Thank you very much!
chapter3.zip (284.6 KB)

[colinbrislawn (Colin J Brislawn)]

Yes! These are probably Illumina's new 'binned' quality scores. They can cause issue with DADA2, sometimes.

NovaSeq and Dada2 incompatibility.

Dear All, I have been analysing NovaSeq 6000 16s rRNA V4-V5 data for the past few months. This is my first experience with NGS data analysis. As a novice, I was sideswiped by the fact that NovaSeq results were very different due to their binned quality scores. From multiple posts, the consensus is that Dada2 is not appropriate for NovaSeq sequences unless you can enforce monotonicity. This leads me to the question, has Qiime2 implemented a way to run the Dada2 denoising algorithm by enforcing …

I would continue with cautious optimism and see how it goes!

which feels like all the sequences are the same

That would be an issue, and you could see that during denoising or during taxonomy assignment. Or maybe it's fine.