phrap quality scores

Stephen R. Lasky srlasky at cellworks.mbt.washington.edu
Fri Jan 7 20:54:13 EST 2000


"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.

Do you have the Phred docs? 

I presume that you don't have the chromats, otherwise you could run them
through phred and get the quality scores.

srlasky
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Stephen R. Lasky, Ph.D.			#
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