I made it through the taxonomy identification but I have 2 questions to make sure that I did everything well.
I am working with COI sequences and followed the moving pictures tutorial. I imported my data, used cutadapt to cut my primers, summarized my data to choose the trunc lenght, and then did the truncation and denoising part using dada2 denoise-paired. After that I created the feature table summary. I followed the tutorial and there is no clustering step, however while reading the tutorial overview it’s stipulated that we should cluster after denoising. Is the clustering done with “dada2 denoise-paired” or did a missed a step? Should I follow another tutorial?
With the feature table summary, I then explored the alpha and beta diversity. After that I trained my database using the midori database for COI sequences and started to explore my data using “taxa boxplot”. In the csv file I have now a number corresponding to my samples and the level chosen. I would like to now if this number is the “number of UNIQUE features”. This is important for my data because I am working with COI. I read about why you are using the word “feature” and what does that means but that part is still not clear for me, sorry. What nomenclature are you using for publishing? Feature?
No, the CSV that you download from the visualization reports the number of sequences assigned to each taxon.
A feature is any kind of observation you have in a feature table. So it could be ASVs, OTUs, metabolites, etc. In your case it would be COI ASVs.
In publication I often use “feature” or “ASV”, but it largely depends on the nomenclature standards of the domain. Maybe check out what they authors used in the COI paper I linked above, and follow what they did?
If you want the number of unique ASVs assigned to each taxon, there is not a straightforward way to accomplish this in QIIME 2, though it would be relatively simple to whip up a solution in R or python, see here for some related discussion: