can we skip this step of specifying position of our desired region, as i dont have primer sequence for my region of interest?
As I can understand that this is just to narrow down our search. correct me if m wrong
What function/command is this in reference to?
please see the following command
qiime feature-classifier extract-reads
Yes, you can skip this step. However, if you want to skip it, I would. recommend just getting a pre-trained classifier if you’re using a standard database.
so shall I use 99_otus.qza in place of ref-seqs.qza while trainning my classifier?
I highly recommend downloading a pretrained classifier for your version of qiime2. There are already full length classifiers made for greengenes and silva. This way, you do the memory intensive process on someone else’s computer.
Otherwise, yes, you would use that as your rep-seq.qza.