I am curios if there is difference on results of using merge or not using merge.
I used the simple 3 samples to compare the results, and found feature-table, sequence, stats' results (after merge and after group) are the same.
So, if anyone has experience or has knowlege to share, I appreciate it.
When working with ASVs, the results are meant to be stable, so this makes sense!
Can you tell us more about your groups and your samples? I think this will provide helpful context to better answer your question.
While we are at it, let's zoom out! What's your biological question?
Thank you @colinbrislawn.
I am new to Qiime2. I have 100 samples of the human microbiome and run all samples at once with dada2. Later, I found the merge option on Qiime and I guess I could save time for various subsets if I run Qiime2 for each sample and merge them. So, I have tried 3 samples first.
For samples on the same run, dada2 should produce equivalent* results wether run on one sample or all!
Let us know if you have any other questions!
*But probably not identical, because