Setting "allowOneOf" and "maxMismatch" parameters in q2/dada2 plugin - Githubissues

qiime2 / q2-dada2

QIIME 2 plugin wrapping DADA2

BSD 3-Clause "New" or "Revised" License

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Setting "allowOneOf" and "maxMismatch" parameters in q2/dada2 plugin #126

Closed francis29029 closed 4 years ago

francis29029 commented 4 years ago

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: https://github.com/benjjneb/dada2/issues/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

nbokulich commented 4 years ago

Hi @francis29029 , Please see https://forum.qiime2.org/ for posting user support questions. Thank you!