I am looking to clarifying how merge-seqs and feature-table merge work for my situation. I have sequence data from different runs, but overlapping sample IDs. Each of these datasets have been demux-ed and deblur-ed separately.
I found that the sequence quality of some samples were better than the same samples in other runs. When merging sequences and tables, will samples with better sequence quality overwrite those that are worse? Otherwise, what is the best approach for this?
Thank you in advance!