I have been trying to decide where to truncate and would value others input.
I think I should truncate forward 280 and reverse 200 to keep the 50th (Median) quality score above 30.
Hello Elizabeth,
Yes, those sound like reasonable settings to me.
Keep in mind that this depends on the length of the region you sequenced, because you still need to leave enough overlap so your reads can join.
After running dada2 with these settings, you can always see which step is removing most of your reads and try to adjust the settings to preserve more of them. More info about how to choose these settings here!
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Thank you for your input and especially for the link.
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