How to draw taxonomy bar chart

[colinbrislawn (Colin J Brislawn)]

Good morning @Shinhyeong_Choe,

Welcome to the forums! :qiime2:

I'm glad you are learning about bioinformatics. There is a lot to learn in the tutorials, and that can be overwhelming at first. Have you done all four tutorials (Moving Pictures, FMT, Atacama soils, and Parkinson’s Mouse)? I ask because there are lots of similarities between them and as you complete all four, you will start to see the common patterns. Some tutorials go into more detail about certain section, which will answer some of your questions.

@Shinhyeong_Choe

Tutorials tell me to set the sequencing depth to take the maximum number of features in the sample while maintaining the maximum number of samples, but I wonder why this will play a big role in future analysis.

That's discussed in more detail in the PD Mouse tutorial#alpha-rarefaction

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I think the 4 main tutorials are the best resource, let me see if I can recommend some other resources for your other questions.

@Shinhyeong_Choe

2. I want to draw a taxonomy bar chart (and diversity index graphs) using R studio

• Tutorial: Integrating QIIME2 and R for data visualization and analysis using qiime2R

@Shinhyeong_Choe

I also wonder how to apply the up-to-date version of the database (where can I find it) for taxonomy analysis.

• Data resources — QIIME 2 2022.8.3 documentation

@Shinhyeong_Choe

• there were comments from experts that comparative analysis was not possible with one sample per sample.

• This is a question about statistical testing, and it depends on your study design (the blocking you used and the groups you want to test). Let's return to this question later!

I hope this helps! Once you have a chance to review the docs and do the tutorials, we can discuss your other questions in more detail.