Hi, i was looking for some advice regarding trimming for DADA2. I was under the impression that you trim where the highest quality is on the plot. I have attached a quality plot from paired end sequencing data. This was a nano run so it doesn't produce as much as a full run.
My question is how do i know where to trim on the forward and reverse read.?
Hi @Mantella86, welcome to the forum!
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!
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