simply run:

make

will generate the binary ready for use. Please visit official site http://methylqa.sourceforge.net/ for documentation.

After get the updated source (either by git pull or downloading the tarbal), run

make clean 
make

will generate the new version of binary. (or make cleanlocal if no changes need for kent and samtools)

Libraries from UCSC Kent source (http://genome.ucsc.edu/admin/jk-install.html) and Samtools (http://samtools.sourceforge.net/) were included in this package. Files were distributed to their own licenses. methyQA currently use Kent source verson v284 and samtools version 0.1.18, the included library here were customized to reduce file size.

Questions or comments, please contact our mailing list (methylQA@googlegroups.com), thanks!

Given a bam file produced by aligning reads to a bisulfite converted reference genome, one can produce the required bed file describing the coordinates of CpG positions and the genome sizes files needed for methylqa bismark mode.

To produce the genome sizes file, use:

create_genome_sizes_from_bam.pl

To produce the cpg bed file, use:

chr_chunk.pl and generate_cpg_bed.pl

This will produce the files needed to run methylqa bismark mode together with the input bam file.