maxEE in dada2 using paired-end data

[Hanna (Han-Na Kim)]

Hi,
I'm running the DADA2 with paired-end data in QIIME2.
I need to use different maxEE options in each forward and reverse strand because poor quality of my reverse strands.
In R version of DADA2, I could set separately each maxEE parameter in forward and reverse strands (e.g. maxEE=c(2,6)).
However, I cannot find independent option of maxEE for paired-end in DADA2 of QIIME2.
When I typed the

$ qiime dada2 denoise-paired --help,

 --p-max-ee FLOAT                [default: 2.0]
                                  Reads with number of expected
                                  errors higher than this value will be
                                  discarded.

How can I apply different maxEE in forward and reverse reads independently?

[benjjneb (Ben Callahan)]

Hi Hanna,
To keep the complexity lower, not all options available through the R version of DADA2 are available through the QIIME2 plugin. Different maxEE thresholds for the F/R reads is one of those unavailable options.

We recommend that you increase the single maxEE value to the level needed to get enough reads through the filter (so perhaps 6 in your case). The forward threshold will be higher than you might have wanted, but this isn't expected to have significant consequences in most cases.

[Hanna (Han-Na Kim)]

Thanks, Ben.

I understand why that is not possible.
As your recommendation, I try to increase the single maxEE.
I also know that the higher level isn't expected to have significant consequences.