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ABI 3700 and Phred/Phrap

Stephen R. Lasky srlasky at cellworks.mbt.washington.edu
Sat Jun 5 20:37:44 EST 1999


Phillip San Miguel wrote:
> 
>     Any problems using Phred/Phrap with the ABI3700 chromat files?  I
> tried Phred out on some DNA standard sequences (*.ab1 files) from the
> 3700 and the histogram of high quality bases gave very low results.
> (Less than 200 bases for all 96 capillaries--even though most of the
> data was pretty good.)
>     Does anyone have any advice?
> Phillip San Miguel
> Purdue Genomics Facillity

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		#
#########################################




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