alpha diversity box plots

[Ricardo Ramiro]

Dear all,

I have a basic doubt about the alpha diversity box plots that are generated after running the core_diversity_analysis.py with standard settings.

I think these boxplots are done using the alpha diversity estimates at the highest coverage from the rarefaction curves. Am I right in thinking this?

Thanks,

Ramiro

[abir...@gmail.com]

Hi, Ramiro,

You are correct.  Under the hood, core_diversity_analysis.py calls (among other things) compare_alpha_diversity.py, and when no explicit depth argument is passed to this script, it defaults to using the deepest available.

Best,

Amanda

[Ricardo Ramiro]

Hi Amanda,

Thank you for your reply. I still have a related question, but I though it would be better for a new topic (here: https://groups.google.com/d/msg/qiime-forum/nttbP32uc24/WKgu4_HBBAAJ)