Using 'qiime quality-filter q-score'

[emmzee]

Hi @colinbrislawn, I saw you that you suggested adjusting the parameters for the qiime quality-filter q-score script, and I was wondering if you could explain to me the --p-max-ambiguous parameter? By default, it is set to zero, but what should I normally look for in my amplicons to adjust it appropriately?

[colinbrislawn (Colin J Brislawn)]

Good morning @emmzee,

Thanks for reaching out! I'm always happy to help.

@emmzee

Sorry to send this to you as a private message - I have been posting on the forum quite often lately and I am afraid of causing unwanted ‘spam’. I know you must be busy, and I appreciate your time and support.

You can always open new topics, as long as your follow the code of conduct, of course!
(It's usually better to keep these posts public, as this let's all the forum member view and answer your question collaboratively.)

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Now on to your question!

@emmzee

I was wondering if you could explain to me the --p-max-ambiguous parameter? By default, it is set to zero, but what should I normally look for in my amplicons to adjust it appropriately?

You can find more detail about that setting in the documentation for that plugin:
https://docs.qiime2.org/2020.2/plugins/available/quality-filter/q-score/
Let me know if that answers your question, and if you have any follow up questions.

More generally, you can find the settings for other plugins on this page:
https://docs.qiime2.org/2020.2/plugins/available/

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I also wanted to mention this

@emmzee

what should I normally look for in my amplicons to adjust it appropriately?

The Qiime 2 developers and plugin developers pick the default settings thoughtfully. If you do want to/need to change them, I would gather evidence that these alternative settings are a better fit for your data set using positive controls.

Because you know reviewer 3 is going to ask 'Why DIDN'T you filter out all reads with ambiguous bases?'

Colin