Let’s say you have a feature table that looks like this:
SampleID feature1 feature2 feature3
s1 7 1 9
s2 3 6 2
s3 0 13 0
The accompanying sequences file would look like this:
and if you attempt to classify those sequences you will get a
FeatureData[Taxonomy] artifact that looks like this on the inside:
So the feature IDs in the feature table, sequences, and taxonomy all correspond. If you use
qiime taxa collapse to collapse your feature table by taxonomy, you would get something like this:
SampleID D_3__Chlorophyta D_3__SomethingElse
s1 8 9
s2 9 2
s3 13 0
So that command will aggregate ASVs that share the same taxonomy, summing their frequencies. But unless if you use that command the ASVs will all remain as distinct features in the feature table.
If you use
qiime taxa collapse, yes, those ASVs given the same assignment are combined. Otherwise, no. (
qiime taxa barplot also sums these together when creating taxa barplots)
All of your ASVs have unique sequences… that’s what makes them distinct ASVs (and their feature IDs are actually unique names that will always be given to that exact same sequence! So if you did the same analysis twice, or merged multiple runs of the same read/trim length and amplicon, you will be able to compare the same ASV in each run)
A single ASV should ideally be assigned the same taxonomy if you attempted to classify it multiple times. Multiple ASVs can receive the same assignment — even at species level — because strain-level differences can exist within the species (I do not know how variable 18S is for plants, but this is usually the case for other amplicons). So ASVs do not always represent unique species, just unique sequences.
I hope that clarifies!