Some of my gz sequence files have _ (underscores) or - (dashes) in the file names. These are appearing to cause issues in the MiSeqSOP: the make.contigs command ends up truncating everything after the _ in the output. Then when I get to the count.seqs command, I get error messages stating I cannot have - in my group names.
I am wondering if can just replace all _ and - in my sequence file names to . (periods). Will that cause any issues in the MiSeq SOP?