Get microbial differences between environmental conditions.
# If taxonomy step is not already done, we need to convert OTU tables into relative abundance taxa tables
# (OTU's annotated by the same taxa are merged and converted to relative abundances)
summarize_taxa.py -i OTU/otu_table_mc2_w_tax_no_pynast_failures.biom -o OTU/Taxa/
# create directory "Stats"
mkdir Stats
# Use Genus (L6) taxa level for getting the taxa showing highest difference between conditions
group_significance.py -i Taxa/otu_table_mc2_w_tax_no_pynast_failures_L6.biom -m metadata.txt -c Treatment -s kruskal_wallis -o Stats/stats_kw.txt
Results:
Stats/stats_kw.txt - table of p-values (and FDR corrected p-values) sorted by taxa of highest impact
Microbial taxa that have a p-values smaller than 0.05 show a significant difference between the conditions in column "Treatment".
-s mann_whitney_u - (Wilcoxon rank-sum test) non-parametric test for comparing two sample groups (control vs. treatment).
-s kruskal_wallis - non-parametric test for comparing more than two groups.
Note: the warning "No metadata in biom table. Won't alter calculations." can be ignored. It's because of using taxa tables instead of raw OTU tables. [qiime google-group]