Error analysis

James VanEe jiv2 at cornell.edu
Wed Mar 28 08:41:05 EST 2001


Hi Maria,
   I use phred to analyze sequencing results and then I use perl count 
up phred q20 scores and record the trim information.  Our sequencing 
group uses this for a quick check.  I've also integrated it into our 
results distribution/management system so the numbers are available 
in a database for reporting. One nice feature is the generation of 
gif images containing a plot of confidence score for each base - very 
useful for identifying and diagnosing problems (what's up with this 
one: http://brcweb.biotech.cornell.edu/funny_gel)  I also used the 
same tools to generate data for the Association of Biomolecular 
Resources' DNA Sequencing Research Group's Never Ending Story.  Say 
that three times fast!  well, the ABRF DSRG NES (not much better, 
huh?) is available here http://nes.biotech.cornell.edu/nes/ and 
you'll see what I mean.  I can send anyone whose interested a copy of 
the perl script I use to run phred and parse the results and the 
details of our distribution system.
A useful tool that we're (DSRG) working on automating is automatic 
alignment of pgem controls to known sequence and counting actual 
errors - it's trickier than it sounds I think. I guess the 3700 
actually has a tool (autoscore) that does something similar 
semi-automated way using.

I'm going to add a rider to this reply; has anyone used ATQA 
(http://www.wagner.com/technologies/biotech/atqaadcopy.html) or 
TraceTuner much?  How do they stack up?  I understand it might be 
tough to compare scores among software even though they might be 
based on a similar log(error) scale.
-James

>Hi everybody,
>
>I am a technician in the sequencing lab of an investigation institute. I am
>interested in doing some kind of error analysis and statistic of my work,
>but I'm not sure wich could be the best way of doing it... 
>someone has a clue and would be so kind of sharing it with me?
>
>thanks a lot!!
>
>Maria
>
>
>---

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James VanEe                              Phone: (607) 254-4862
BioResource Center
Computing Facilty
170/171 Biotech Bldg                       Fax: (607) 254-4847
Cornell University
Ithaca, NY 14853                 www: http://brcweb.bio.cornell.edu
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