Hi-C Matrix Quality Control

关于

Evaluate the quality of Hi-C contact matrices with this comprehensive QC tool designed for .mcool, .cool, and .hic formats. The skill automates the calculation of critical metrics like cis/trans ratios and distance-dependent contact decay (P(s) curves), while generating visual reports to assess coverage uniformity and library complexity. Whether checking a single sample or correlating multiple biological replicates, this skill ensures genomic data meets the rigorous standards required for downstream analyses such as TAD calling, loop detection, and compartment analysis.

主要功能

• Pairwise replicate correlation analysis for biological reproducibility assessment
• Automated visualization of coverage histograms and P(s) scaling curves
• Standardized QC metrics including coverage, cis/trans ratios, and contact decay curves
• Support for .mcool, .cool, and .hic file formats with automated conversion
• Harmonization of chromosome naming and genome assembly alignment
• 2 GitHub stars

使用场景

• Standardizing quality reporting for genomic contact matrix processing workflows
• Determining if Hi-C data quality is sufficient for advanced structural genomics analysis
• Measuring and visualizing experimental consistency between biological replicates