phred training and capillary questions

Stephen R. Lasky srlasky at u.washington.edu
Tue Oct 26 16:18:26 EST 1999


Bionetters.  I keep hearing that phred isn't trained on the 3700, as a
matter of fact, I think I've said it myself.  But what do we really mean
by that?  I know what our results show; phred calls the high quality
bases well, but seems to assign lower quality to bases at >500 than they
appear to be by eye.  After assembly with Phrap, these reads go into
assemblies well and the number of reads to get the same coverage doesn't
seem to have increased.  So what is it that we mean by phred not being
trained, and does it really need more training? 

If phred really needs more training, maybe those of us who use 3700's
need to start putting pressure on PEBiosystems to supply Phil Green and
his team with an instrument to train phred on (what chance is there of
that?). I know he already has one of the other flavors of capillary
machines.

In this same vein, I was wondering what kind of experiences people with
capillaries are having? We have two 3700's here and have had abysmal
uptime and pass rate records on them (let's be generous and say 75%
uptime (and that's being really generous)).  Has anyone had the
opportunity to run 3700's alongside MegaBACEs?  How do you feel about
the MegaBACE?  What kind of life span are people getting out of the
capillaries from both machines? Have other people done an estimate on
the cost per lane or cost per Q>20 base from the capillaries as opposed
to 377s? If there are problems with capillary clogging on the MegaBACE,
do you think its is because of your DNA prep, and how have you modified
it to accommodate the capillary machines.

I was also wondering if the ABRF is putting together a QC report on the
capillary machines?  If anyone knows, it would be nice to pass it to the
group.  With the kind of throughput you can get from capillaries, it
seems like a fairly controlled sample could be generated very quickly so
we could compare the 1999 flat plate results with the almost-2000
capillary results. (?).  

thanks

srlasky
-- 
Stephen R. Lasky, Ph.D.			#
University of Washington		#
Department of Molecular Biotechnology	#
HSB K324 box 357730			#
Seattle, WA, 98195 USA			#
email:	srlasky at u.washington.edu	#
Phone: 	206-616-5865			#
Fax:	206-685-7301			#
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