DADA2 trimming?

Hi @Mantella86, welcome to the forum! :smile:

That's a great question! There is no hard and fast number, but as a general rule it's best to trim/truncate your reads where you are seeing a general drop in your average quality score. The interactive quality plot is definitely a good tool to use for visual inspection, and I appreciate you sharing those screenshots!

This is ultimately up to you and your judgement on the quality score that you want to use as a cutoff, but I'd say that you would probably want to truncate somewhere between 140-150 for your reverse reads (since we see a drop in the average quality score after that), and then most likely between 170-180 for your forward reads (since the quality score drops substantially after that, and there are big gaps in the available data).

Here's another forum post that discusses this topic as well, for reference. Hopefully this helps inform your decision on where to truncate your reads!

Cheers,
Liz

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