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)