[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.


More information about the Autoseq mailing list

Send comments to us at biosci-help [At] net.bio.net