Paired-end bsaliged files were generated using Methy-Pipe. Methy-Pipe can be downloaded from https://sunlab.cpy.cuhk.edu.hk/methy-pipe/
Please also install bedtools intersect (avaliable @ https://bedtools.readthedocs.io/en/latest/content/installation.html)

1) Prepare sample.info (#SampleID, Type, path_to_W.bsalign.file, path_to_C.bsalign.file)
2) Prepare mouse.ref.size files and revise bin/BSalign2bed_with_motif_mm9.pl accordingly (here contains mm9.size.fa for demonstration)
3) Run the program
	sh genmk.sh > makefile 
	nohup make -j 5 all &   
4) Output files: sample.region.profile & sample.end.density.pdf  
