Peak calling

CPT3: An Integrated Package for ChIA-PET, HiChIP and PLAC-Seq data analysis.

peak calling

CPT3 contains peak calling method with MACS2 (suggest) or SPP method.

$ java -jar ChIA-PET.jar --macs2 macs2 \
macs2 path, using macs2 callpeak to detect anchor peak with alignment file. default: N

Tip

For feature requests or bug reports please open an issue on github.