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.
Requirements:
1.
Java(TM)
SE Runtime Environment
2.
Software1:
Bedtools
3.
Data1:
reference.fasta
4.
Data2:peaks
called from peakcaller (MACS )
Result:
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
Group：http://bioinformatics.csu.edu.cn/