could you please suggest are these parameter ok for dada2: I understand that trim parameter is used to remove primer sequences from forward and reverse read, do I need to remove these sequences here as quality of sequencing is not bad.
--p-trim-left-f 19 --p-trim-left-r 20 --p-trunc-len-f 249 --p-trunc-len-r 204
You should remove primers from your reads regardless of their quality.
I would also consider truncating some more from your 3’ ends if you can afford it, as in if you have enough overlap to allow you to truncate them. That is because your quality starts to dip on those tail ends and without truncating those, dada2 is more likely to discard those reads completely prior to denoising.
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