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Apr 17, 2018
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#2560 to master #2561

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9 changes: 8 additions & 1 deletion qiita_pet/support_files/doc/source/analyzingsamples/index.rst
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Expand Up @@ -54,12 +54,19 @@ Rarefying Features
.. figure:: rarefy.png
:align: center

* **Rarefy features** :ref:`[11]<reference11>` , :ref:`[12]<reference12>` : Subsample frequencies from all samples without replacement so that the sum of frequencies in each sample is equal to the sampling-depth
* **Rarefy features**: Subsample frequencies from all samples without replacement so that the sum of frequencies in each sample is equal to the sampling-depth.

* **BIOM table** (required): Feature table containing the samples for which features should be rarefied
* **Parameter set**: Parameters at which the rarefication is run
* **Sampling depth** (required): Total frequency that each sample should be rarefied to, samples where sum of frequencies is less than sampling depth will not be included in resulting table

Note that rarefaction has some advantages for beta-diversity analyses
:ref:`[11]<reference11>`, but can have undesirable properties in tests of
differential abundance :ref:`[12]<reference12>`. To analyze your data with
alternative normalization strategies, you can easily download the raw biom
tables (see :doc:`../tutorials/downloading`) and load them into an analysis
pipeline such as `Phyloseq <https://bioconductor.org/packages/release/bioc/html/phyloseq.html>`__.

Filtering Samples by Metadata
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

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