Two BED files for CpG sites from Watson and Crick strands are required by the script of bin/methylation_vs_size.mm9.pl
Those BED files can be generated by 
	 perl bin/extract_CpG_site.pl <outprefix> <ref.genome.fa> 
For demonstration, here contains beds files for subset CpGs sites in mouse chromosome1 (mm9.Chr1.C.rev.CG.bed & mm9.Chr1.W.CG.bed)

1) Prepare sample.info (#SampleID, Type, path_to_W.bsalign.file, path_to_C.bsalign.file)
2) Run the program
	sh genMDsize.sh > makefile
	nohup make -j 5 all &
3) output files: sample.meth & sample.MD.vs.size.pdf
