I have more than one sff file because we used a divided plate.
Is it correct to run the “Schloss SOP” on every file and at the end compare the different outputs obtained (diversity, etc)?
Or is it necessary to merge the files from the beginning?
Thanks a lot.
If you’re following the Schloss SOP, then I would merge the files after running trim.seqs. If you run the same sample on the different plates, then you might modify your group names in the oligos files to indicate rep1 and rep2. You can always modify this later to merge or average the two reps.