OTU abundance threshold - 0,005% of what

General Discussion
3

Hi,

thanks for your reply. I will try to make my question clearer.

The paper I am referring is titled " Quality-filtering vastly improves diversity estimates from Illumina amplicon sequencing" by Bokulich et.al.: https://www.nature.com/articles/nmeth.2276

My question is about what is defined as “secondary filtering / OTU abundance threshold ©” in the cited paper.

I understand from reading other posts on the forum that OTU-abundance threshold filtering is no longer recommended if using deblur/dada2 Filter Feature Table .

Although not recommended any longer in QIIME2 I would really appreciate if you could help me understanding the 0,005% OTU abundance filtering approach, as it is used in a lot of microbiome studies. I have not been able to understand clearly if it is 0,005% of all reads in the entire sequencing run, or 0,005% of all reads in one sample.