CpG-based Peak Detection of ChIP-seq

Min Li1, Wenjing Zhang1, Yu Tang1, Yi Pan1,2, Fang-Xiang Wu1,3, Jianxin Wang1*

1School of Information Science and Engineering, Central South University, Changsha, 410083, China.

2Department of Computer Science, Georgia State University, Atlanta, GA 30302-4110, USA.

3Division of Biomedical Engineering and Department of Mechanical Engineering, University of Saskatchewan, Saskatoon, SK S7N 5A9, Canada


CpGpeak, a peak detection method using the characteristics of CpG islands. Unlike the traditional peak detection methods that rely entirely on experimental data statistics and simulation results, CpGpeak combines the information of the genome with the experimental data of ChIP-seq.



1.       Java(TM) SE Runtime Environment

2.       Software1: Bedtools

3.       Data1: reference.fasta

4.       Data2:peaks called from peakcaller (MACS )



The result contains top 50 predicted drug-target interacton

The first column is the target ID and the second column is drug ID



1.Use MACS(or other peakcallers) to deal with your datasets and get the peak regions(peak.bed)

2.Run the program : sh CpGpeak.sh hg19.fasta peak.bed out_name


OutFile format:

Chr start end peak_ID MACS_P-value CpGpeak_P-value Combined_P-value


Software download: CpGpeak.zip

Test data download: test.bed





Please feel free to contact us for any questions . mail:wjzhang@csu.edu.cn