I have a quick question, just want to verify the pipeline for removal of the Chloroplast and Mitochondria from my 16s samples.
I have used the filtering tutorial to remove both the chloroplast and mitochondria from my Bacteria-table.qza file, using qiime taxa filter-table and was able to see that these taxonomic groups were in fact removed. My question is, do I need to remove these taxonomic classifications from the actual taxonomy file as well? What about the rep-seq file? Does it matter, and or how do I know which files need to be passed through the filters? (I know it’s a lot of question, so thank you in advance).
I looked over the forum, but mostly found questions on how to filter out these taxonomic classes and I want to make sure that I do not miss any steps (I also cannot ask my labmates, since they have yet to work on Qiime2).
**If possible, and if this makes it easier for you, please let me know if there are specific websites and or articles I should read so that I do not bug you guys as much.
Thanks a million