HiCRes

HiCRes estimates and predicts Hi-C library resolution to quantify how sequencing depth affects chromatin interaction map resolution for experimental design.

Key Features:

• Resolution Estimation: Provides a framework for estimating the current resolution of Hi-C libraries to inform analyses of gene expression regulation and DNA replication in a cell-type specific manner.
• Predictive Capability: Predicts how additional sequencing depth will improve library resolution to guide experimental planning.
• Flexible Input Options: Accepts BAM files with genome indices (for faster processing) or raw sequencing FASTQ files as inputs.

Scientific Applications:

• Experimental design and sequencing depth optimization: Estimates required sequencing depth to reach target Hi-C resolution for planned experiments.
• Chromatin interaction analysis in model organisms: Supports analysis and planning for human and mouse Hi-C datasets, including libraries prepared with MboI, HindIII, or Arima protocols.

Methodology:

Applies a mathematical framework for estimation and prediction of Hi-C resolution and is provided as a Docker pipeline.