Diversity Metrics

Hello.
Perhaps I missed this somewhere in the documentation. Is there an equivalent for a parameters file from qiime1 where you can list the alpha and beta diversity metrics that you want as output so you can provide this to the “core-metrics” command from the diversity plug-in? Or separately to “alpha” or “beta” ? When I looked in the help, it does looks like there is a way to provide a “config” file, but not sure if this is the same thing or how to prepare this document.

Alternatively, can you list several metrics in the alpha or beta command? I was unsuccessful when I tried this approach with a variety of delimiters.

Thanks,

Trina

Hi @taknotts!

At the moment you can only supply one metric at a time to alpha, alpha-phylogenetic, beta, and beta-phylogenetic, but we will hopefully have support for supplying more metrics at runtime in the future. We will update this thread when that is supported (I have opened an issue to track this development!). In the meantime, you will need to run your command (e.g. alpha) multiple times — once per metric (sorry for the inconvenience).

Hi @thermokarst !
Thank you for the info. I have always assumed that when you passed a parameter file to the core_diversity_analyses.py command in qiime1 that it used the same rarefied set of sequences for the calcs of all the metrics (table_even####.biom). In qiime2, I did not see where I could pull this rarefied table to use for the additional set of measures I want to run. Is there a way to get the table of rarefied sequences that was used for the core-metrics set?

If it’s not possible, I assume that I would need to perform 3 steps, rarefy first, then alpha, then provide the rarefied table to core-metrics?

Thanks,

Trina

Hi @taknotts!

This is an oversight on our part, we have an open issue to start returning the rarefied table as part of core-metrics.

Close, but not quite!

If you rarefy yourself, then you won’t want to use that table as input to core-metrics, which assumes you are providing it an unrarefied tabled. You will have to rarefy, then use alpha, alpha-phylogenetic, beta, and beta-phylogenetic as necessary to compute all the metrics and stats you are interested in. Once core-metrics supports returning the rarefied table, then you would just run core-metrics using your unrarefied table, then grab the rarefied table that is output and feed that into whatever other methods you want, but again, this isn’t implemented just yet. Sorry for the extra hurdle at the moment!

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In the 2017.9 release, core-metrics and core-metrics-phylogenetic now include the rarefied table in the results! :tada:

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