Loop calling¶

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

Loop calling

Loop calling ¶

CPT3 can obtained .

CPT3 can calling loops with three different mode.
1. calling loops with ChIP-Seq peaks

$ java -jar ChIA-PET.jar --INPUT_ANCHOR_FILE sample.peaks_narrowPeak \
 a file which contains user-specified anchors for interaction calling. If you dont have this \
 file, please specify the value of this variable as null instead. Default: null.

1. calling loops with MACS2 peak detect by CPT3

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

1. calling loops with SPP method

$ java -jar ChIA-PET.jar \
dont define --INPUT_ANCHOR_FILE and --macs2 paramaters.

Tip

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