Analyzing Different sample batches in the same sequencing run

Hello, and thank you for making this forum. I've learned a lot by reading the discussions here!
I have a question that might be very simple, but it's confusing me.
I work on soil samples. I have three different sites, and I have a set of samples from each site. I had one sequencing run for all the samples ( all in one plate, V3-V4, Illumina 2*300 bp). Now, suppose I want to analyze each site separately. In that case, I'm assuming I should analyze the sequences from those sites separately? since if I use the other sites' sequences files, they might affect my trimming, filtering, sampling depth, etc...
On the other hand, if I want to compare three sites later on, can I use my results from the separate analysis for each site, or should I do another analysis with all the files from all the sites? In that case, would it be problematic for my separate site analysis since the parameters might be different?

Thank you!

Since Dada2 will perform better with more samples from the same run, you can run dada2 for all samples and create a feature table, that can be filtered according to your metadata files. Representative sequences can also be filtered by already filtered feature tables.
However, if your machine cannot handle all samples, as a second and less advisable option you also can divide samples by datasets before Dada2.

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