Good morning:
I recently conducted an experiment to evaluate the toxicological effect of metal-containing water on microbial communities using mesocosms. However, I found a high relative abundance of chloroplasts, should I remove them for taxonomy analysis? If so, is there a tutorial on the subject?
Try this!
https://docs.qiime2.org/2024.10/tutorials/filtering/
While you are doing the search, consider searching for forums for 'chloroplast' and see how others handle it. Let's me know if you find a method that might be a good fit for your data!
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