Hi, Anyone knows if there is a way to count how many (phylum, classes, genera, species,...) were assigned? Or i have to do that manually?

Hi Mary, Following the methods suggested by Nicholas, you should get what you need. If you want to know the number of taxa detected in each sample, below is an example at the genus level using feature table and taxonomy file from the "Moving Pictures" tutorial. # Collapse feature table at genus l…

Hi Mary, I'm not aware of direct commands to implement it in QIIME2 but you can export results and make a phyloseq object in R. Then you can use the following codes kindly shared by Mike Mclaren to do the calculation at the reads and ASV level. [tax_assigned] Yanxian

Hi @yanxianl , Thank you for your reply. But i would like to know how many classes, species and so on, exist in my taxonomy and not the number of reads. Is it possible to do that with qiime?

Do you want to know how many taxa were detected in each sample? If yes, just use qiime taxa collapse, then run qiime diversity alpha --p-metric observed_otus and the counts will be taxa counts at whatever level you collapsed to. [image] MaryAnn: i would like to know how many classes, species a…

Hi, @Nicholas_Bokulich I want to know for example: my sample has 20 classes, 90 genus and 160 species. These are the numbers that i want to know

which QIIME2 artifact should i download?

If you mean the feature table and taxonomy file used in the example, you can find them in the QIIME2 tutorial " Moving Pictures ". For your own data set, use the feature table (e.g., table.qza) and taxonomy (e.g., taxonomy.qza) you got from your analysis. If you want to do it in R, follow the qiime2…

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number of taxa (class, phylum, species,...)

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