Bisulfite sequencing results - how to analyze (May/01/2006 )
I've done some bisulfite sequencing by 'cloning then sequencing'. Just to see if this worked, I only picked 3 colonies - 2 colonies have 22 CpG dinucleotide (out of 41) are methylated while the other colony shows a different pattern of methylation (20 at different CpG sites).
1) Does this mean one allele is 53% methylated (22/41) and the other allele is 48% methylated (20/41)? Or, it means there are mix population of cells in which some cells are 53% while some are 48% methylated?
2) How to present/analyze the results as degree of methylation?
Thanks for any help and suggestion.
3 colonies is not enough to guage anything really, you would need to sequence more.
There is a program called BiQ Analyzer writte by Christoph Bock that makes presenting such data, a whole lot easier. Google it and download the program it's pretty simple to use!
You could always manually draw an array of circles to represent all 44 CpG sites and fill the ones in that are methylated, that is what you usually see in the papers.
Here is the link