Create two OTU .biom tables with selected subset of samples# create two new OTU tables, containing samples only of diet_A or only of diet_B (Treatment column)filter_samples_from_otu_table.py -i otu_table_mc2_w_tax_no_pynast_failures.biom -o
otu_A.biom -m metadata.txt -s
'Treatment:diet_A'
# create related subset metadata mapfiles for A and B (Treatment column 4) awk -F"\t" '$4=="diet_A"||NR==1{print}' metadata.txt > metadata_A.txt awk -F"\t" '$4=="diet_B"||NR==1{print}' metadata.txt > metadata_B.txt Remove control samples from OTU .biom table# remove all control samples: keep all '*' , but not '!' Control samples (Treatment column) filter_samples_from_otu_table.py -i
# metadata mapfiles without "Control" samples (take all lines with Treatment column 4 not equal != "Control") awk -F"\t" '$4!="Control"||NR==1{print}' metadata.txt > metadata_without_Control.txt http://qiime.org/scripts/filter_samples_from_otu_table.html |