PET divide

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

PET dividing

CPT3 can divide paired reads into valid pair reads, self-ligation reads and other- pair reads based on interaction distance or restriction endonuclease sites and fragment.

• divide pair reads based on interaction genomic distance (valid for ChIA-PET and HiChIP data)

• divide pair reads based on restriction endonuclease sites and fragment (valid for in-situ ChIA-PET and HiChIP data)

$ java -jar ChIA-PET.jar --SELF_LIGATION_CUFOFF 8000 \
specifies the distance threshold between self-ligation PETs and intra- chromosomal inter-ligation PETs. \
Default: 8000 for ChIA-PET data, 1000 for HiChIP data.

Tip

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