Hi.
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.
Hello @Jhlee,
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? 
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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.
Ah ok!
DADA2 builds an error model for each sequencing run, so it's best to run it separately on seperately runs. See this form post and this part of the dada2 tutorial.
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! 
EDIT:
*But probably not identical, because
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