dada2: how to set "allowOneOf" and "maxMismatch" parameters in q2/dada2 plugin ?

[Francis29029 (francis)]

Setting “allowOneOf” and “maxMismatch” parameters in q2/dada2 plugin · Issue #126 · qiime2/q2-dada2

Hello,

We were used to work with dada2 1.10 and now we want to move to q2 (2019.10) using the DADA2 plugin embedded in q2.

By reading carefully? the documentation of the dada2 plugin (https://docs.qiime2.org/2019.10/plugins/available/dada2/denoise-paired/) we did not find how to adjust the following parameters :

• allowOneOff of the DADA2 removeBimeraDenovo method (following this discussion: benjjneb/dada2#610)

• maxMismatch in the DADA2 mergePairs method (we prefer this over having a fixed quality score / sequence length cutoff)

Is there any way to edit these parameters in q2/dada2 ?

Thanks a lot

Francis

[Nicholas_Bokulich]

Hi @Francis29029,
Thanks for re-posting your question to the forum!

You are correct, these options are not exposed in the release version of q2-dada2 at the moment, though they could be useful (we are always open to contributions to the repo ) .

However, q2-dada2 is just running an R script under the hood — so it would be possible to:

1. clone the q2-dada2 repo from github
2. modify that R script to edit these options
3. install your local branch of q2-dada2 as a development version in your QIIME 2 environment (you may want to create a separate development environment for this to keep it separate from your standard QIIME 2 release environment)
4. proceed

I hope that helps!

[Francis29029 (francis)]

@Nicholas_Bokulich

q2-dada2

Thanks Nicholas, it helps (not straightforward but worth to try)

[Francis29029 (francis)]

@Nicholas_Bokulich

modify that R script to edit these options

Hello, I am struggling a bit to find out exactly which R script exactly to be modified, do you have any idea by chance ?

[Nicholas_Bokulich]

Assuming you are using denoise-paired