Can DADA2 be carried on pre-joined reads

Hi @sindhu_mohandas,

The Moving Pictures tutorial is actually using V4 region, but the only thing that would really change is your denoising step as it requires different consideration in the truncating parameters of DADA2. This is well covered through various other threads on the forum.

It looks like you have already seen the great tutorial here that shows exactly how to train your own classifier. You should follow that tutorial closely right from the beginning.
The command you have above needs to be completely modified to match your case. For example, you need to include your own primer sequences and not the one in the tutorial as those are specific to the V3 region. Also as mentioned in one of the highlighted blue 'note boxes' in that tutorial, with paired-end reads you end up with reads that are variable in length and so it is recommended that you don't actually do any truncating when extracting your reads. Another point that is also in the tutorial, do not use 85% green-genes otus file, that is just for the sake of the tutorial.
Have a read there and let us know if you have any other questions. Good luck!