In dada2 denoise-paried, there are option;
–p-max-ee-f NUMBER Forward reads with number of expected errors higher
than this value will be discarded. [default: 2.0]
–p-max-ee-r NUMBER Reverse reads with number of expected errors higher
than this value will be discarded. [default: 2.0]
what does the error mean? the mismatch, or the low quality score?
Thank you!
Hi @ranxx005,
The maxEE parameter there is the expected error allowed in each read. maxEE has been shown to more effective in filtering poor quality reads than averaging quality scores. This is why DADA2 default of q-score is set to only 2, because it relies on maxEE instead to deal with poor quality reads. The original paper describing maxEE can be found here.