hic-loop-calling

Detect chromatin loops from mcool or hic files by providing a sample name, genome assembly, and data path to automate extraction and loop calling. The workflow outputs BEDPE loop calls and supporting view files.

You can call Hi-C loops at a specific resolution with cooltools by specifying a loop-resolution input. The workflow extracts contact matrices at your chosen resolution and generates BEDPE loop files.

Hi-C loop calling can fail due to inconsistent chromosome names, so this workflow harmonizes chromosome names to the "chr" convention. This standardization ensures proper coordinate matching during contact matrix extraction and loop calling.

You do not need to manually generate chromosome-arm view files for Hi-C loop detection. The workflow automatically generates these temporary view files for downstream analysis and visualization in IGV.

The best way to automate BEDPE loop calling from processed Hi-C data is using an end-to-end workflow that validates inputs, harmonizes coordinates, extracts matrices, and runs loop calling. This delivers reproducible BEDPE loop calls and view artifacts.

This loop calling workflow supports cool and hic formats besides mcool. It accepts processed Hi-C inputs in .mcool, .cool, or .hic formats to produce BEDPE loop calls and temporary view files.