[Bioperl-l] chromatogram

Scott Cain cain.cshl at gmail.com
Thu Nov 15 09:21:26 EST 2007

Hi Lee,

Distributed with GBrowse is Bio::Graphics::Glyph::trace, which uses
Bio::SCF to draw trace files onto a Bio::Graphics::Panel.  Bio::SCF is
not part of bioperl, so you have to get it from CPAN and it depends on
the Staden io-lib package, so you'll need that too.  You can get GBrowse
from http://www.gmod.org/gbrowse , and you can look at the tutorial for
more information on configuring the trace glyph.


On Thu, 2007-11-15 at 08:24 -0500, Lee Katz wrote:
> Thank you all.
> Are you all sure in that there is no way to go from an scf to an image
> though?  I do have abi files, but I am relying on Phred output for
> base calls for other things and I want to stay consistent.  This means
> that if I use the fasta files that I get from Phred in another part of
> my program, I need to use the scf files it produces.
> If this is not possible, do you know if drawing an scf is in the works?  Thanks.
Scott Cain, Ph. D.                                         cain at cshl.edu
GMOD Coordinator (http://www.gmod.org/)                     216-392-3087
Cold Spring Harbor Laboratory

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