I’m about to order a set of dual index primers. I vaguely remember there being a warning on one of the earlier versions of the wetlab SOP about which primer plates to combine if you are running less than 384. did you find that it was not actually an issue or do you just always run 384?
The index sequences must balance the number of bases at each position. The index sequences listed in the SOP have a ~25% ATGC composition at each site. If you are going to cherry pick indices from the list, make sure that you have even representation. Here’s the updated SOP: