I understand it is possible to calculate the consensus sequence using IUB codes, but is it possible to display IUB codes within the contig editor?
I have recalled the bases of sanger sequences using tracetuner to label mixed bases with IUB codes, then mapped them to a reference sequence with MIRA. When I view the SCF trace files I can see the degenerate bases, however they are displayed as a dash "-" within the contig editor. I would like to see these in the contig editor so they can be considered for the consensus sequence.
I can't recall what Gap4 does with these, but I think it varied based on the consensus method being used. If you're using quality values they'll just get treated as N though. Gap5 discounts these at present for certain.
I'm not sure how we'd mix IUB codes with qualities. I assume those bases have quality 0 anyway.