Note: methylQA used R statistical environment for plotting figures and LaTeX document preparation system for generating PDF report, so it's necessary to have these two tools installed first: (install example commands for Ubuntu)

# install R
sudo apt-get install r-base 
# install LaTeX
sudo apt-get install texlive-latex-base texlive-latex-extra

Get the source and compile

Users could download the latest stable release of methylQA package at Download, after downloading and decomressing, run a make command would generate the binary program file ready for use:


Users are also encouraged to use git to get the latest developmental version of methylQA package:

$ git clone git://
# go to the methylQA folder
$ cd methylQA/
# then run a make command here
$ make
# the binary methylQA file will be generated
# (optional) you can put the methylQA binary at you $PATH directory for easy use

Support Files

Files for Human hg19

chomosome size file: hg19_full.size

chomosome size file without supercontigs: hg19_lite.size

CpG bed file: CpG.bed.gz

CpG bed file without supercontigs: CpG_no_contig.bed.gz

MRE fragments file (3 enzymes): TriMRE_frags.bed.gz

MRE fragments file (5 enzymes): FiveMRE_frags.bed.gz