[Automated-sequencing] quality scores using consed/phrap/phred

Sampson, Joshua (NIH/NCI) [E] via autoseq%40net.bio.net (by Joshua.Sampson from nih.gov)
Thu Oct 22 09:09:17 EST 2009


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.

Josh



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