Redo analysis with ref-hit files; various fixes

Closes #1. One of the big things worth noting is that I filtered out Chloroplast and Mitochondrial hits from the table before running Songbird/Qurro. This reduces the number of mostly-irrelevant features in the analysis. (Can of course redo songbird/qurro runs with just table.qza if desired.)
knightlab-analyses · Sep 27, 2019 · bfd4aa1 · bfd4aa1
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diff --git a/.gitignore b/.gitignore
@@ -1 +1,2 @@
 gg_13_8_99*.qza
+.ipynb_checkpoints/
diff --git a/AnalysisOutput/qurro-plot.qzv b/AnalysisOutput/qurro-plot.qzv
diff --git a/AnalysisOutput/rep-seqs-summary.qzv b/AnalysisOutput/rep-seqs-summary.qzv
diff --git a/AnalysisOutput/rep-seqs-unfiltered-summary.qzv b/AnalysisOutput/rep-seqs-unfiltered-summary.qzv
diff --git a/AnalysisOutput/rep-seqs-unfiltered.qza b/AnalysisOutput/rep-seqs-unfiltered.qza
diff --git a/AnalysisOutput/rep-seqs.qza b/AnalysisOutput/rep-seqs.qza
diff --git a/AnalysisOutput/songbird-differentials.qza b/AnalysisOutput/songbird-differentials.qza
diff --git a/AnalysisOutput/songbird-regression-biplot.qza b/AnalysisOutput/songbird-regression-biplot.qza
diff --git a/AnalysisOutput/songbird-regression-stats.qza b/AnalysisOutput/songbird-regression-stats.qza
diff --git a/AnalysisOutput/songbird-regression-summary.qzv b/AnalysisOutput/songbird-regression-summary.qzv
diff --git a/AnalysisOutput/table-no-mitochondria-or-chloroplast.qza b/AnalysisOutput/table-no-mitochondria-or-chloroplast.qza
diff --git a/AnalysisOutput/table-summary.qzv b/AnalysisOutput/table-summary.qzv
diff --git a/AnalysisOutput/table-unfiltered-summary.qzv b/AnalysisOutput/table-unfiltered-summary.qzv
diff --git a/AnalysisOutput/table-unfiltered.qza b/AnalysisOutput/table-unfiltered.qza
diff --git a/AnalysisOutput/table.qza b/AnalysisOutput/table.qza
diff --git a/AnalysisOutput/taxonomy.qza b/AnalysisOutput/taxonomy.qza
diff --git a/Mackerel 16S Data Analysis.ipynb b/Mackerel 16S Data Analysis.ipynb