Problem: The number of Samples where certain species is present isn’t same before and after filtering the features using --p-min-frequency.
Background: I filtered the features which min frequency is 18 from table.qza and based on filtered-table.qza,
I filtered the features from rep-seqs.qza and then assigned the taxonomy using trained GreenGenes data (gg-13-8-99-515-806-nb-classifier.qza)
code for filtering the table.qza.
qiime feature-table filter-features \
–i-table table.qza \
–p-min-frequency 18 \
–o-filtered-table filtered-table.qza \
I was comparing the number of Samples where certain species at level 4 was present before and after filtering the features with min frequency (18).
I saw the discrepancy in the number of samples it was observed in before and after filtering. For example:
This species k__Archaea;p__Crenarchaeota;c__MBGA;o__NRP-J was seen in 140/180 samples before filtering but it was only present in 135/180 Samples after filtering.
Could you please help to figure what I am missing?