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References for direct sequencing - (May/22/2006 )

Hi, everyone!

I have done some direct sequencing of bisulfite modified DNA recently and now I need some information on the analysis of data. Does anyone know any papers where this method rather than analysis of individual clones was used?

I have found only this one, however the authors used a special software to analyse sequencing traces:

Quantitative DNA methylation analysis based on four-dye trace data from direct sequencing of
PCR amplificates
Jörn Lewin, Armin O. Schmitt, Péter Adorján, Thomas Hildmann and Christian Piepenbrock
Bioinformatics, Vol. 20 no. 17 2004, pages 3005–3012

I wonder if it would be correct simply to measure peak heights in the chromatogram?
Thank you for any help!


that is pretty much correct to measure peak height,

The Clark group have also extensively done measurements this way but have only grouped each CG methylation status in five categories 0%, 25%, 50%, 75%, 100% and their most recent paper can be found here

There isn't really a special program to do this apart from manually measuring it.

good luck