I'd certainly be interested in the results. I think success might
depend on whether this adjustment (normalization?) for assumed
composition happens in the same stage as mobility adjustments and
whatnot that take the raw florescence data and change them to the
peaks we know and love. I believe phred is starting from the
processed peaks given to it by the abi (or other) software - the
damage might be done at that point. There are alternatives for the
intitial processing steps, but I can't list them off the top of my
head with any authority. the phred papers (genome research
8:175-185) mention "plan" (B. Ewing and P. Green, in prep.) but I
couldn't find a published paper. I know I've come across other "lane
processors": BASS
(http://www.genome.wi.mit.edu/ftp/distribution/software/Bass/doc/BASS.html)
or maybe these are something to build on (but I notice they are not
currently available:
http://ravel.zoology.wisc.edu/sgaap/Bioinformatics.htm
>Hi Bob,
>
>Have you tried an different software program that might have a different
>basecalling algorithm? One possibility is to analyze the results with
>phred. If you do not have phred readily available, just send me some
>chromatogram files and I would be happy to give it a try.
>
>ABI should take note that many labs would love to use flourescent
>sequencing to detect methylayed C's. Nice trick regarding the hidden menu
>for 377s. Did you find it by randomly banging the keyboard in fustration?
>
>- George
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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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