Hi-C Compartments Calling (MCP-based)

Overview

This skill provides an automated workflow for compartments calling on .mcool, .cool or .hic Hi-C data.

Main steps 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 compartments. ~50-250 kb is recommended. 100 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.
Perform PCA-based compartment analysis and extract the first principal component (PC1).
Generate compartment interaction saddle plots and BigWig outputs for visualization.

Use this skill when: