ITS-metabarcoding, denoised data

Welcome to the forums! :qiime2:

Thank you for posting your full commands and DADA2 output stats. It looks like most reads are being removed during filtering, so let's work to improve that.

Have you viewed the sequences-trimmed.qzv file? This will show you quality throughout the read.
I usually trim off the low-quality ends of the read, which helps more reads to pass the quality filter.

See this post for more details: Why do I have more sequences (therefore more taxonomic groups recovered) when I use only my forward sequences ? - #4 by SoilRotifer

Let us know what you try next and if you have more questions!

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