quality scores using consed/phrap/phred

[Sampson, Joshua (NIH/NCI) [E]]

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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[Sven Klages-2]

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
>
> _______________________________________________
> Autoseq mailing list
> Autoseq@...
> http://www.bio.net/biomail/listinfo/autoseq

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[Phillip San Miguel]

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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