Hi-C Loop Calling

Overview

This skill provides a minimal and efficient workflow for detecting chromatin loops from Hi-C data stored in .mcool format and preparing results for visualization in IGV. The key steps involved include:

• Refer to the Inputs & Outputs section to verify required files and output structure.
• Always prompt user for genome assembly used.
• Always prompt user for resolution used to call loops. ~2-50 kb is recommended. 5 kb is default.
• Locate the genome FASTA file from homer genome fasta file based on user input.
• Rename chromosomes in the .mcool or .cool file to satisfy the chromosome format with "chr".
• Generate chromosome-arm view files for compartment calling after changing the chromosome name.
• Extract contact matrices from .mcool files at the desired resolution.
• Detect chromatin loops.

When to Use This Skill

Use this skill when: