HiCUP

HiCUP maps and filters sequencing reads from Hi-C and Capture Hi-C (CHi-C) experiments to a specified reference genome to produce artifact-filtered interaction data for downstream analysis of three-dimensional genome organization.

Key Features:

• Supported experiments: Processes sequence data derived from Hi-C and Capture Hi-C (CHi-C) experiments.
• Independent end mapping: Performs independent mapping of each end of an interaction pair to improve mapping precision.
• Reference-genome mapping: Maps interaction reads onto a specified reference genome.
• Artifact removal: Identifies and removes experimental artifacts from Hi-C/CHi-C datasets.
• Quality-control reporting: Generates comprehensive QC reports that summarise data quality and experimental metrics.
• High-quality interaction retention: Retains high-quality interaction data for downstream chromosomal interaction analyses.

Scientific Applications:

• 3D genome organization analysis: Preparation and filtering of Hi-C and CHi-C datasets for studies of chromosomal interactions and spatial genome architecture.
• Preprocessing for downstream analyses: Produces artifact-filtered interaction datasets suitable for downstream interaction calling and interpretation.

Methodology:

Performs independent mapping of each read end to a specified reference genome, filters and removes experimental artifacts, and generates comprehensive quality-control reports.