Parameters Description


(Meha) #1

Hello dear friends,
Hope you are doing well!

I am still having an issue regarding some parameters’ descriptions in every method. Honestly, I do not understand the concept of the explanation what exactly each tells us.
For example in this method:
https://docs.qiime2.org/2019.1/plugins/available/dada2/denoise-single/

the parameters are puzzling to me, for example:

–p-min-fold-parent-over-abundance FLOAT
–p-n-reads-learn INTEGER
–p-hashed-feature-ids / --p-no-hashed-feature-ids
–cmd-config FILE
–verbose
–quiet
–citations

I do not know their meanings, and I do not know are they necessary or not! The descriptions in front of some parameter are insufficient to learn more. I request you humbly to suggest me an extra source to understand them when I need them.

Thank you very much!


(Nicholas Bokulich) #2

@Mehrdad,
All QIIME 2 actions have required and optional parameters. The help documentation mentions whether a parameter is required or optional. In general, the default parameter settings (i.e., for optional parameters) are set to provide all-around good performance and should not need to be changed unless if you know what you are doing. You should really only be worrying about required parameters.

The parameters you have listed are optional parameters. If you really want to change these, and if the QIIME 2 help documentation is unclear, you should read the dada2 documentation for more details about what those parameters do.