h4HiChIP-Peaks

h4HiChIP-Peaks identifies enriched peaks in HiChIP datasets using a re-ligation site representation to enable robust loop-anchor detection and quantitative comparison of peaks across samples.

Key Features:

• Re-ligation site-based peak identification: Represents HiChIP data by re-ligation sites to improve reliability and recall of peak detection, including at reduced sequencing depth and with lower false discovery rates.
• Enhanced loop-anchor detection: Uses identified peaks as robust anchors for downstream loop calling tools to improve chromatin looping discovery.
• Quantitative cross-sample comparison: Counts reads mapping to peaks across samples to enable differential peak analysis.

Scientific Applications:

• Chromatin architecture and gene regulation: Supports analysis of 3D chromatin organization and regulatory interactions from HiChIP data.
• Chromatin looping studies: Improves detection of loop anchors for investigations of looping mechanisms.
• Differential peak comparison: Enables quantitative comparison of peak enrichment between samples or experimental conditions.

Methodology:

Represents HiChIP data centered on re-ligation sites for peak identification, uses identified peaks as anchors for downstream loop calling tools, and performs read counting over peaks across samples to facilitate differential analysis.