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compare_alpha_diversity.py uses the wrong number of degrees of freedom when it performs the t-tests. This results in p-values that are much higher than they should be.
In qiime.compare_alpha_diversit…
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# without taxa
caporaso@saguaro make_otu_heatmap> make_otu_heatmap.py -i otu_table_no_tax.biom
Warning: The lineages are missing from the OTU table. If you used single_rarefaction.py to create your…
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Currently pree.py doesn't comply to pep8. It is an easy fix but would make the code more readable as well as pass linters.
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See [this discussion](https://github.com/gregcaporaso/student-microbiome-project/wiki/Timeseries-filtering).
Are there additional filtering combinations that we want to include?
Thanks @jrrideout f…
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When running guppy rarefaction or squash but not for pca or compress. The offending jplace file is available from:
http://www.cs.wisc.edu/~darling/concat.trim.jplace.bz2
This is using the latest revi…