Dear, I hope you are well, I would like to know in which file or what command I can execute to know how many ASVs were taxonomically assigned in my data set. I will appreciate your help.
Hello @Wen,
Check out this section of the PD-Mouse tutorial
https://docs.qiime2.org/2022.2/tutorials/pd-mice/
I think the outputs of qiime metadata tabulate
or qiime feature-table tabulate-seqs
would both be able to answer you question by adding up the list of ASVs in their tables.