Removal of Chloroplast and Mitochondria (Verification of pipeline)

[fabipc (Fabiola)]

Hi

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

[timanix (Timur Yergaliyev)]

Hi! I think, you already done everything in right way, so you can proceed with the analysis without any worries

[fabipc (Fabiola)]

Sweet! One last question, just to verify, since I want to calculate the diversity metrics on qiime2 and I have to use the rep-seqs file, wouldn’t I have to remove the chloroplast and mitochondria from these file as well?

[timanix (Timur Yergaliyev)]

It’s not necessary since you removed it from your table.qza

[fabipc (Fabiola)]

I see, so the rep-seq table will follow the format of the table. Perfect!

Thanks again for all your help