ABI 3700 and Phred/Phrap

Herve Crespeau crespeau at genoscope.cns.fr
Thu Jun 10 12:15:37 EST 1999


> Stephen R. Lasky wrote :
>
> We've been running phredPhrap on the 3700 files and gotten pretty good
> results (when I called Q>20 values of about 400 by eye, phred called 406
> and 422 (for eg)).  Lee Rowen has talked to Brent Ewing about retraining
> phred on 3700 chromats.  It turns out that Genoscope has sequenced and
> submitted (and is therefore presumably high quality sequence) a bac on
> chromosome 14 that overlaps one of our bacs by a significant amount, so
> we are going to run 10-12 plates of sequence on the 3700 and use the
> Genoscope sequence as a known and give Brent the dataset.  
> 
> Bottom line is that we'll have to wait a bit to see if any changes in
> phred are necessary.
> 
> srl
> 
> -- 
> Stephen R. Lasky, Ph.D.			#
> University of Washington		#
> Department of Molecular Biotechnology	#
> srlasky at u.washington.edu		#
> #########################################
> 
Thanks for the newsgroups to consider our sequences as "hight quality", and usable as 
references. But you should be aware of the fact that the BAC sequences actually submitted by us 
on chromosome 14 are in HTGS, that means they do not yet conform to the Bermuda rules for 
quality.

I think you can compare your sequences with the interior parts of our contigs, but the 
extremities of the contigs should be taken with caution.

If you need more information, please do not hesitate to contact us.
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