A question is raised in my mind, then I need to take advantage of your idea and experience.
To draw an acceptable and well-analyzed taxa bar plot in terms of science in Qiime2 or any software package, should I essentially and scientifically pass the alpha-, beta diversity and rarefaction steps before? Can I publish unrefined reads/taxa bar-plot without scientific error and any risk?
One more question crossed my mind before creating the topic. Should I use unverified reads for alpha and beta diversity? What if I use ratified reads for them?
I would greatly appreciate your feedback.