Application of cLoops2 to HiChIP data with H3K4me3 and Arima Hi-C kit

[COOL005]

Hi,

I am working with H3K4me3 HiChIP data generated using the Arima Hi-C kit. The pre-processing of the raw paired-end reads was done with HiC-Pro. Would cLoops2 be suitable for downstream analysis of this HiChIP data, including loop calling and differential interaction analysis?

Any guidance would be appreciated.

Thank you!

[YaqiangCao]

Hi,

I am working with H3K4me3 HiChIP data generated using the Arima Hi-C kit. The pre-processing of the raw paired-end reads was done with HiC-Pro. Would cLoops2 be suitable for downstream analysis of this HiChIP data, including loop calling and differential interaction analysis?

Any guidance would be appreciated.

Thank you!

Hi,
cLoops2 can work with H3K4me3 HiChIP data but can not guarantee best performance, please refer to here figure S12&S13 for a demo with H3K27ac HiChIP data.
To process with HiC-Pro results, please use ![hicpro2bedpe.py] (https://github.com/YaqiangCao/cLoops2/blob/master/scripts/hicpro2bedpe.py) to process into BEDPE file, then just follow the cLoops2 readme to run any other analysis.
Good luck and have fun.
Best,
Yaqiang