phrap quality scores

[Stephen R. Lasky]

"Rachel M. Kadel-Garcia" wrote:
> 
> In article <387698C5.EEA17FB at cellworks.mbt.washington.edu>,
> Stephen R. Lasky wrote:
> >"Rachel M. Kadel-Garcia" wrote:
> >>
> >> Does anyone here have an understanding of phrap quality scores
> >> beyond what's in the docs?  I'm trying to figure out how to
> >> assign similar quality scores to assemblies not done with phrap,
> >> and I'm resorting to spelunking in the source, but it's rough
> >> going.
> >>
> >>                                                 Rachel
> >
> >
> >Phrap, I believe, is not the program assigning the quality scores.
> >Phred is.  Phrap uses the phred quality scores to do its alignments.
> 
> Phred assigns quality scores to bases in individual reads.  Phrap uses
> those quality scores and various things about the alignments to generate
> consensus quality scores.
> 
>

Sorry, you are correct.  Phrap does assign a quality score for the
concensus sequence based on the quality of the raw data (phred q score)
and the extent of confirmation of the base by other reads.

I do not know how to deconvolute that score.

srl

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Stephen R. Lasky, Ph.D.			#
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