Let me open with the standard disclaimor that I'm new to these packages and therefore apologize if i'm submitting an obvious question.
I have received a set off .SFF files that I would like to process/align.
Running consed gives me an .ace file with fragments and their starting points in the reference sequence. This is great.
However, I would also like the quality score for every base in every fragment (not just the consensus sequence). If I had chromat files, I could see how to do this with Phred. However, all I have is the .SFF files. Any suggestions on how to get the Phred Quality Scores for the fragements?
Any help would be greatly appreciated.