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

Sven Klages via autoseq%40net.bio.net (by klages from molgen.mpg.de)
Thu Oct 22 11:09:24 EST 2009


Hi Joshua,

if you use current consed's add454Reads.perl it's
doing everything for you.

After opening the ace file you can normally work with
your sequences ..

Sorry, I don't see the problem!?

cheers,
Sven


+++ Sampson, Joshua (NIH/NCI) [E] (22.10.2009 16:09):
> 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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