Thanks in advance for your help. I could not find the answers to my questions in the forum, I apologize if you already discussed this issues.
I have a couple of questions regarding the rarefaction.
1-I love the alpha rarefaction visualization! How can I download the plot instead of the csv data?
2- In qime1 I used to create a rarefied OTU table for the downstream analyses. How can I create a rarefied table in qiime2?
Thank you for your kind attention and your help!
I usually take screenshot of the plot, I am not aware of a way to save the plot as image from that visualiser.
The plug in to rarefy the data is the following:
If you use any of the beta-diversity pipeline, this plug in is used behind the scene, so in the output folder you should find the rarefied data that has been used for all the diversity analyses: ‘rarefied_table.qza’.
I am pointing this out because if you repeat the rarefaction steps many times (even using the same rarefaction threshold) you will get every time slightly different results because the random nature of the selection (although the main finding should be the same!).
Hope it helps
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