Prerequisite
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:
make
Users are also encouraged to use git to get the latest developmental version of methylQA package:
$ git clone git://github.com/lidaof/methylQA.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