What I want to ask is that if I collect the 16S SRNA data from 200 samples on the NCBI website, and I have grouped the data by type, not by primer, but by process type, and now when I look at the statistics, I see that some of the primers are different from one group to the next, how do I use qiime2 to deal with this, even if the primers are the same, but some of them are different in terms of base pairs? The purpose of my research is to compare the differences in microbial communities between different processes, how do I do that?
Hello!
If the only difference are some basepairs, you can process the whole dataset together. Make sure that the primers end with the same DNA sequence to ensure that ASVs will be compatible.
I would compare primers, make that they end at the same position, delete primers separately for each batch / sequencing run, run Dada2 also separately, but with the same settings. Then you can merge feature tables and representative sequences.
Some differences are expected because of differences in primers, but, as I understand, you are interested in exploring such differences.
Best,
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