make_otu_table.py –i combined_seqs_otus.txt –t rep_set_tax_assignments.txt –o raw_otu_table.biom
Then I ran a command to filter singletons and doubletons
filter_otus_from_otu_table.py -i raw_otu_table.biom -o out_table_temp.biom -n 3
filter_otus_from_otu_table.py -i otu_table_temp.biom -o out_table.biom –-min_count_fraction 0.00005
- Dolores Sanchez