Fig. 4: Systematic representation of the bioinformatic analysis and the pipelines used in this study. | Communications Biology

Fig. 4: Systematic representation of the bioinformatic analysis and the pipelines used in this study.

From: Improved cohesin HiChIP protocol and bioinformatic analysis for robust detection of chromatin loops and stripes

Fig. 4

Raw HiChIP data were processed using three independent pipelines: (1) Juicer27, (2) nf-HiChIP, and (3) ChIA-PIPE29. The outputs generated from these pipelines were subsequently utilised as inputs for specialised analytical tools, including APA analysis, Stripenn30 and gStripe for stripe detection, and LoopSage32 for 3D genome modelling.

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