I know that we should use 30 overlapping bases at least. But, I don’t know about if there is a maximum. I have 2x250 paired end data and quality scores for all positions are over 25, so I’m not sure if I should truncate it or not.
Amplicon size is 292, so if I don’t truncate at all, I end up with 208 overlapping bases. Do I need to cut it down to a number?
Since I’m still new about this and I haven’t understood the context clearly I end up with such questions.
What do you suggest about this?