too many zeros in 16S rRNA amplicon sequencing data

Question

[zhangdengwei]

Hi all,

I have some 16S rRNA sequencing data from human tissue, which was performed on NovaSeq 6000 platform. I detected ~40000 ASVs in total after removing singletons. However, most ASVs were only present in a few samples. In other words, ~95% ASVs are Zero in one specific sample. Those huge numbers of Zero significantly prevent me from downstream analysis.

Whether removing low frequent ASVs is also a controversial topic. Could anyone give me some advice? Thanks!

[andres.firrincieli]

You have too many ASV (40k) and I think this is a problem related to the denoising (DADA2) of NovaSeq 6000 sequencing data. Maybe this post could be helpful: link

[zhangdengwei]

Exactly. I agree that this is due to the NovaSeq which is not very compatible with qimme2 DADA2 pipeline. I finally surrendered to other approaches.