qiime2 / q2-dada2

QIIME 2 plugin wrapping DADA2

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

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Add more DADA2 parameters to the wrapper #99

Closed apcamargo closed 5 years ago

apcamargo commented 6 years ago

For some types of analysis it is desired to tweak some DADA2 parameters that are not available in the QIIME 2 wrapper, such as BAND_SIZE, OMEGA_A and OMEGA_C (the latter is only available in version 1.8).

I recently did a analysis with ITS2 data, which required me to change the BAND_SIZE. Because of that, I had to run the denoising step in R and then import the results into QIIME 2.

Maybe we could start a discussion of which parameters could be added to q2-dada2.

ebolyen commented 6 years ago

51 may also be relevant to the conversation. It seems like DADA2 has a bunch of functionality which would be great to expose in a more granular way (with all of the new parameters). As well as having some easy pipelines which do most of the work for simple situations.

benjjneb commented 6 years ago

Happy to take suggestions. We will be doing an update once dada2 1.8 is released on Bioconda (July maybe) letting us transition the plugin to the latest R package release

OMEGA_A, BAND_SIZE and pool seem to me like clear candidates to expose.

benjjneb commented 5 years ago

At this point in time I'm not planning on exposing OMEGA_A or OMEGA_C in the plugin. I am planning on adding a pool parameter with the dada2v1.10 update.