Basically I want to trim DNA sequences using forward and reverse primer set. The trimmed sequences still contain the forward and reverse primer but what before and after would have been trimmed off
Two strategies would be: 1) "Perfect match then trim": i.e. find the location in the sequences that are perfect match to forward and reverse primers, then do the trim; I wrote a script can do it very well; 2) "Fuzzy match then trim", i.e. when searching the primer matching strings in the sequences, allow up to 2 mismatches, and then trim the sequence; I have a difficult time to do so; Bio::Grep can perform the fuzzy search, but how should I trim the seq and print the trimmed sequence out?
Thank you all for any suggestions.