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Use same rarefactions for alpha both errors
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When using alpha_rarefaction.py with the observed_species metric (which is non-phylogenetic), the workflow failed at the alpha_diversity.py step because the alpha_diversity.py commands contain '-t Non…
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1). Split each OTU into sample and control tables to determine which negative control otus to substract
a). echo "split_otu_table.py -i /home/gifl2111/scratch/SMP/split_otu_table_by_body_site/Fore…
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It would be very useful to be able to keep/discard OTUs from the OTU table using a list of sequence identifiers. I have many sequences that do not align to reference databases and it would be nice to …
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From Holly Menninger:
"I've spent a lot of time thinking about how to make complex ideas digestible for the general public. We've been working on a similar challenge as you all with our home microbio…
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Some users would like the ability to show every 1K seqs on the x-axis, however; for large datasets, by default it just chooses by max and shows about 10 values instead of numerous values at every x nu…
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Just a few updates needed in the QIIME Overview Tutorial, the tutorial will most likely work with latest version, there is just one thing that changes. The whole document makes reference to a OTU Tabl…
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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.