[Bioperl-l] Bio::SeqIO::scf traces scrambled?

Chris Fields cjfields at illinois.edu
Thu Jun 18 16:27:02 EDT 2009

On Jun 18, 2009, at 3:02 PM, Charles Tilford wrote:

> Cook, Malcolm wrote:
>> Charles,
>> Another possible stopgap that might work for you, if you're working  
>> with AB1 chromatograms and have ABIs kb-basecaller turned on, is to  
>> use Bio::Trace::ABIF
>> 	http://search.cpan.org/dist/Bio-Trace-ABIF/lib/Bio/Trace/ABIF.pm
>> It works great and includes implementation of ABIs algorithm  
>> allowing to (re)compute trace clear ranges using kc-basecallers  
>> quality scores and any windowing/quality parameters.
>> Its not in the bioperl project but it is an easy install from CPAN.
> Thanks - we installed that a few weeks ago, and it was on my list of  
> things to try, but I had not gotten to it yet since I was getting  
> data out of the SCF SeqIO module. Even though the SeqIO::scf data  
> looks ok, the fact that I need to unscramble it makes me nervous...  
> Thanks, too, for the example code. I'll try out the Bio::Trace::ABIF  
> module and see if it works with our files.
> Thanks,

You definitely shouldn't need to unscramble it; my guess is this is a  
legit bug that just has gone unnoticed.  I see that you have filed a  
ticket on it so we can at least track it.  Thanks!


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