Hello all, I'm demultiplexing reads from a MiSeq run and I'm having some doubts regarding the barcode detection using Flexbar 3.5. As far as I could understand from the manual, using the parameter '--barcode-error-rate' you can change the threshold for mismatches and gaps, but not one or the other. I would like to allow a certain % of mismatches, but not gaps. Is it possible?
Also, flexbar uses Needleman-Wunsch algorithm for the alignments, with +1 score for a match, -1 for a mismatch and -9 for a gap as default, but what is the 'magic score' to keep or discard a read? I could not find that in the manual or in the article.
Any thoughts on the matter will be helpful!