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

Phillip San Miguel via autoseq%40net.bio.net (by pmiguel from purdue.edu)
Thu Oct 22 11:36:07 EST 2009


Sampson, Joshua (NIH/NCI) [E] wrote:
> 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
> 
Hi Joshua,
  sff files are generated by a Roche 454 sequencer. Fasta and qual info 
can be extracted from them using sffinfo -- a program Roche provides.

Use sffinfo -h to get the documentation.
-- 
Phillip



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