I checked my taxonomy barplot, there, chloroplast and mitochondria are present. So I have removed those. but I am thinking this I should have removed before alpha and beta diversity analysis.
Is it so?
when should we exactly filter these contaminants?
It is better to remove them (of course, if you are not interested in them) before any analysis from table.qza since they can really affect the results.
No need to filter rep-seq.qza
but we should also remove these from rep-seq file because we are also using the same.
We are using them, but all calculations are performed on the data in table.qza. Rep-seqs should contain all id’s from table.qza, but it’s not bad if you have data in rep-seq.qza that are not in table.qza anymore
again I got one doubt.
taxonomy.qza file that we are using for filtering out contaminants. and generating a new table and that table we will use for further analysis.
and when you come to the taxonomic analysis, again generating taxonomy.qza file and proceed.
Isn’t it so confusing?
Usually I perform taxonomic analysis before any other analyses, after I obtain all necessary files. Then I filter my tables, including removing of mitochondria and chloroplasts, then I perform the rest of analyses, using already created (before filtration) rep-seq and taxonomy files.