# Filter out the samples with less than 22000 reads
qiime feature-table filter-samples \
--i-table ../DADA2_denoising_output/table.qza \
--p-min-frequency 22000 \
--o-filtered-table temp0.qza

# Filter samples from the group
qiime feature-table filter-samples \
  --i-table temp0.qza \
  --m-metadata-file ../metadata.tsv \
   --p-where "Group1='T_Control' OR Group1='cB_	Control'" \
  --o-filtered-table temp1.qza

# Filter features that only appear in a single sample
qiime feature-table filter-features \
--i-table temp1.qza \
--p-min-samples 2 \
--o-filtered-table temp2.qza


# Filter features based on frequency
qiime feature-table filter-features \
--i-table temp2.qza \
--p-min-frequency 20 \
--o-filtered-table temp3.qza

# Collapse table at genus level
qiime taxa collapse \
--i-table temp3.qza \
--i-taxonomy ../classified_rep_seqs.qza \
--p-level 6 \
--o-collapsed-table feature_table_for_ANCOM_genus.qza

rm temp0.qza temp1.qza temp2.qza temp3.qza

# Add pseudocount
qiime composition add-pseudocount \
--i-table feature_table_for_ANCOM_genus.qza \
--o-composition-table ANCOM_ready_table.qza

# Run ANCOM 
qiime composition ancom \
--i-table ANCOM_ready_table.qza \
--m-metadata-file ../metadata.tsv \
--m-metadata-column Group1 \
--o-visualization ancom_Group1_results_genus.qzv \
--verbose