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