Number of ASVs per sample

[Benedict (Benedict Tan)]

Dear all,

I was in confusion about the output of DADA2. I noticed that the FeatureTable[Frequency] provides the number of seq counts (frequency) in each sample, but not the count of each unique seq - ASV in each sample.
For instance, the feature table summary in the moving picture tutorial listed out:-
Number of samples: 34
Number of features: 770
Total frequency: 153,884
Is number of feature equivalent to number of ASV? I was only able to view ‘Feature Count’ per sample in the “Interactive Sample Detail” tab and I believe that it is number of total frequency (feature X number of appearance) per sample, am I right?

I did check the similar topic in q2-forum and there’s a suggestion where Observed OTU computed via core-metrics phylogenetic workflow can generate my desired output. Yet, it is computed on rarefied datasets, isn’t it? Is there any way to produce the initial ASV number per sample without any rarefaction?

-Benedict-

[Mehrbod_Estaki]

Hi @Benedict,
You're right that those visualizers do not provide a summary of # unique features/ASVs per sample.

@Benedict

Is number of feature equivalent to number of ASV?

Correct! Features and ASVs are interchangeable terms here.

If you are interested in how many unique ASVs/features are present in each sample, then as you already have read you can achieve this by calculating the observed_otus metric using the qiime diversity alpha action. This doesn't require rarefying. A rarefying depth is only needed if you use the core-metrics phylogenetic pipeline which calculates alpha diversity and various other metrics.