How to set p-perc-identity with UNITE dynamic reference sequences?


I am trying to use qiime vsearch cluster-features-closed-reference command for ghost tree and I am wondering how I should set --p-perc-identity if I am using a unite dynamic reference sequences since dynamic uses either 97% or 99%. Can I set a range?



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Hello Andrew,

The flag --p-perc-identity is the minimum percent, so if you set it to 90%, many reads should still match at 97 and 98 and 99%. The question is would you rather have a read match at 91%, or be dropped from the tree all together.

(The ‘dynamic’ cluster distance of Unite does not make a big difference to the vsearch plugin.)



Thank you for the clarification!

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