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!