Hi-C Contact Matrix QC for .mcool Files

Overview

This skill performs QC on Hi-C matrices stored in .cool or .mcool format files at a user-selected resolution.

Main steps include:

• Refer to the Inputs & Outputs section to check required inputs and set up the output directory structure.
• Always wait the user feedback if required files are not available in the current working directory by asking
  "${files} not available, provide required files or skip and proceed ?"
• Inspect the .mcool file to list available resolutions and confirm the analysis resolution with the user.
• Compute coverage and cis/trans ratios.
• Assess coverage uniformity across bins from coverage tables.
• Compute cis expected contact frequency and distance-dependent contact decay (P(s) curves).
• Visualize contact decay and P(s) scaling curves.
• If multiple Hi-C replicates are provided, compute pairwise correlation of balanced matrices at the chosen resolution.
• Summarize QC metrics and plots into a structured output directory.