dada2 paired end denoising max overlapping base

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?

Hi @the_dummy,

There isn’t a lot of harm in more overlap, since, depending on your joining method, you get more confidence in the overlapped regions (if they match, its even more evidence that your bases are correct!)

So, I don’t think Id do additional trimming.



Thank you very much for clearing my mind.

1 Like

This topic was automatically closed 31 days after the last reply. New replies are no longer allowed.