Convert OTU tables into relative abundance taxa tables1) OTU's annotated by the same taxa are merged and converted to relative abundances2) Relative taxa abundances are visualized as bar plots summarize_taxa_through_plots.py -i OTU/otu_table_mc2_w_tax_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/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) |
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