see a paper here Conserved DNA methylation patterns in healthy blood cells and extensive changes in leukemia measured by a new quantitative technique http://www.tandfonline.com/doi/full/10.4161/epi.22552

Does any have experiences with this type of data and have scripts to extract methylation levels after alignment? I know probably after bowtie mapping and using pysam to get the reads ratio for reads start with CCGG (methylated) and GGG(unmethylated).

Just in case someone has written scripts for it.

Thanks, Ming