We have three separate runs (Ion Torrent) that we would like to do diversity analysis on, but as I mentioned there are barcodes that have been used in multiple samples, i.e. Barcodes 1, 2, 3, and 4 were used in Runs A, B, and C. We cannot simply merge the .sff files and then do analysis because this would lump samples that are different into one barcode set.
What would be the best course of action?