Bacon

	step1: Read alignment & PET filtering	step2: call peaks & count loops	step3: Estimate significance
HiC-Pro	√	-	-
MAPS	√	√	√
HiChipper	-	√	√
FitHiChIP	-	√	√
CID	-	√	√
cLoops	-	√	√
HiCCUPS	-	√	√

HiC-Pro

Servant N, Varoquaux N, Lajoie BR, Viara E, Chen C-J, Vert J-P, Heard E, Dekker J, Barillot E. 2015. HiC-Pro: an optimized and flexible pipeline for Hi-C data processing. Genome Biol 16: 259.

Command line

HiC-Pro -i /mES-hichip -o /mES-hicpro_out -c CONFIG

HiC-Pro -i /k562-hichip -o /k562-hicpro_out -c CONFIG

Hichipper

Lareau CA, Aryee MJ. 2018. hichipper: a preprocessing pipeline for calling DNA loops from HiChIP data. Nat Methods 15: 155.

Command line

hichipper --out mES-hichipper_out mES.yaml

hichipper --out k562-hichipper_out mES.yaml

Juric I, Yu M, Abnousi A, Raviram R, Fang R, Zhao Y, Zhang Y, Qiu Y, Yang Y, Li Y, et al. 2019. MAPS: Model-based analysis of long-range chromatin interactions from PLAC-seq and HiChIP experiments. Plos Comput Biol 15: e1006982.

Command line

Bash ./run_pipeline_mES.sh

Bash ./run_pipeline_K562.sh

FitHiChIP

Bhattacharyya S, Chandra V, Vijayanand P, Ay F. 2019. Identification of significant chromatin contacts from HiChIP data by FitHiChIP. Nat Commun 10: 4221.

Command line

bash FitHiChIP_HiCPro.sh -C configuration_mES

bash FitHiChIP_HiCPro.sh -C configuration_k562

CID

Guo Y, Krismer K, Closser M, Wichterle H, Gifford DK. 2019. High resolution discovery of chromatin interactions. Nucleic Acids Res 47: gkz051-.

Command line

java -Xmx32G -jar gem.jar CID --data /hicpro_mes.rmdup.bedpe --g mm10.chrom.sizes --micc 2 --out /ChIA-PET2_mes_mis1_CID

java -Xmx32G -jar gem.jar CID --data /hicpro_k562.rmdup.bedpe --g hg19.chrom.sizes --micc 2 --out /ChIA-PET2_k562_mis1_CID

cLoops

Cao Y,Chen Z, Chen X, Ai D, Chen G, McDermott J, Huang Y, Xiaoxiao G, Han J-DJ. 2019. Accurate loop calling for 3D genomic data with cLoops. Bioinformatics.

Command line

cLoops –f /hicpro_mes.rmdup.bedpe -o /mes_hichip_cLoops -eps 2500,5000,7500,10000 -minPts 10,15,20 -hic.

cLoops –f /hicpro_k562.rmdup.bedpe -o /k562_hichip_cLoops -eps 2500,5000,7500,10000 -minPts 10,15,20 -hic.

HiCCUPS

Durand NC, Shamim MS, Machol I, Rao SSP, Huntley MH, Lander ES, Aiden EL. 2016. Juicer Provides a One-Click System for Analyzing Loop-Resolution Hi-C Experiments. Cell Syst 3: 95–98.

Command line

hiccups -m 1024 -r 5000,10000 K562.hic hiccups_results