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Taxonomy

Convert OTU tables into relative abundance taxa tables

1) OTU's annotated by the same taxa are merged and converted to relative abundances
2) Relative taxa abundances are visualized as bar plots
summarize_taxa_through_plots.py -i OTU/otu_table_mc2_w_tax_no_pynast_failures.biom -o Taxa/ -m metadata.csv

Or, to get only relative abundance tables (1) without additional visualization (2)
summarize_taxa.py -i OTU/otu_table_mc2_w_tax_no_pynast_failures.biom -o Taxa/

Results


1) Relative abundance taxa tables
Taxa tables as .biom and .txt format for different taxonomic levels.

ls Taxa/
otu_table_mc2_w_tax_no_pynast_failures_L2.biom  # L2 - Phylum
otu_table_mc2_w_tax_no_pynast_failures_L2.txt  
otu_table_mc2_w_tax_no_pynast_failures_L3.biom
  # L3 - Class
otu_table_mc2_w_tax_no_pynast_failures_L3.txt  
otu_table_mc2_w_tax_no_pynast_failures_L4.biom  # L4 - Order
otu_table_mc2_w_tax_no_pynast_failures_L4.txt
otu_table_mc2_w_tax_no_pynast_failures_L5.biom  # L5 - Family
otu_table_mc2_w_tax_no_pynast_failures_L5.txt   
otu_table_mc2_w_tax_no_pynast_failures_L6.biom  # L6 - Genus
otu_table_mc2_w_tax_no_pynast_failures_L6.txt   



2) Relative abundance bar plots for each sample (summarize_taxa_through_plots.py)
Taxa/taxa_summary_plots/bar_charts.html  (to open in web-browser)