A portion of my gz succession documents have _ (highlights) or - (runs) in the record names. These are seeming to cause issues in the MiSeqSOP: the make.contigs order winds up shortening everything after the _ in the result. Then when I get to the count.seqs order, I get blunder messages expressing I can’t have - in my gathering names.
I’m contemplating whether can simply supplant all _ and - in my arrangement document names to . (periods). Will that cause any issues in the MiSeq SOP?