I'm new to qiime2. I visualized the imported data and found that the interactive quality plot is a little strange. It does not show a histogram like that in the tutorial, but a small horizontal line. Is there anyone who can answer me? thanks very much? i were struggled for it for weeks. that's so painful.
Hello and welcome to the forum!
Such quality plots are usual for new Illumina technologies, such as NovaSeq. The differences are connected with new quality scores system, so it looks different on the plots.
There are some concerns about how it will affect Dada2 performanc: Consequences of using dada2 on NovaSeq data · Issue #791 · benjjneb/dada2 · GitHub.
Basically, you can implement solution from the issue above or proceed as it is with some possible bias in your data. I did both variants with several datasets some time ago and didn't noticed significant changes, so usually I just use Dada2 in Qiime2 as it is. But you should be aware of this issue before you will proceed.
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thanks for your fast reply!! so as you reply, this interactive quality plot is normal, or i can say the data which imported was perfect?
Quality plots are fine for NovaSeq 6000 or similar Illumina techniques. In other words, there is nothing wrong with it.
thank you vvvvery much for your reply!!!
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