I have a doubt regarding the filter-out of chloroplasts and mitochondria after the taxonomic classification. I understood that the sequences belonging to these ASV/OTUs should be also removed from the table.qza and rep_set.qza. After the filter out of these sequences, the phylogenetic tree is constructed again, without the chloroplast and mitochondria sequences. The logical reason is that if they are in the tree, they affect the results of the diversity analysis.
Should I also removed from the original data before and run the dada2 command from the scratch? How these sequences could affect the algorithm in dada2 steps?
Thanks in advance!