Combining MeDIP-seq and MRE-seq to investigate genome-wide CpG methylation

. Author manuscript; available in PMC: 2016 Jan 15.

Published in final edited form as: Methods. 2014 Nov 6;72:29–40. doi: 10.1016/j.ymeth.2014.10.032

Name	Purpose	Website for download and documentation
Cutadapt	Adapter trimming and quality filtering of raw reads	https://code.google.com/p/cutadapt/
BWA	Align raw or filtered reads to the corresponding genome assembly	http://bio-bwa.sourceforge.net/
Samtools	Operating on read alignment files	http://samtools.sourceforge.net/
R	Statistical computing environment	http://www.r-project.org/
methylQA	Parsing aligned reads, generating bed files and bedGraph files.	http://methylqa.sourceforge.net/
methylMnM	Calculating differentially methylated region (DMR) between two samples by integrating MeDIP-seq and MRE-seq data.	http://epigenome.wustl.edu/MnM/
methylCRF	Predicting methylation level at single CpG resolution by combining MeDIP-seq and MRE-seq data.	http://methylcrf.wustl.edu/