It would be nice to be able to leave the forward primer in the sequence, rather than having it automatically trimmed off. In my study, the forward primer is designed with some taxonomic selectivity, and is important for later classification of sequences.
two options - don’t include the forward primer in teh oligos file or put a # at the beginning of the line. either way the primer won’t be removed. hope this helps.
pat
Yes, but I would still like to cull those sequences that don’t have a perfect primer match…