Thank you for your kind support. I have viewed the table.qzv at QIIME 2 View QIIME 2 artifact, and in particular the Interactive Sample Detail tab in that visualization. Now I am confused which value I will choose to pass for--p-sampling-depth? How many samples will I have to exclude from my analysis? I have three replicates for each treatment. I am attaching table.qzv file with this message. Kindly view and suggest me a valid sampling depth. Also guide me why we use this parameter?
The choice of your sampling depth is entirely dependent on your experiment. This question has been covered in the forum a few times already, for example you can read about them: here, here, and here for starters.
In your dataset 6,595 is your lowest sample which is fairly good for most common communities, so you might be ok keeping all your samples at that depth. Again, it is entirely dependent on your experiment and what information you are trying to get. Please have a read through the existing forum discussions on the topic and let us know if you have any additional questions.
