Hi-C

Hi-C is a chromatin conformation capture technique used to study the 3D organization of the genome. It measures the spatial proximity between DNA regions, producing interaction maps that reveal topologically associating domains (TADs) and other structural features.

In this tutorial, we’ll build a Hi-C processing pipeline using the AI bioinformatics agent. The pipeline consists of three stages:

1. BWA-MEM — Align paired-end reads to the reference genome
2. pairtools — Process alignments into filtered, sorted pair files
3. cooler — Convert pair files into cool files for visualization and downstream analysis

Installing Nodes from the Extension

All the nodes used in this pipeline can be installed from the Bioinformatics Hub extension. Simply press Install, and it will download all the necessary files to your current working directory (the one selected in the file explorer) and automatically load the nodes into your node bar — complete with example workflows.

In this tutorial, we’ll use the pre-built Hi-C flow that comes included with the extension.

:::note Don’t forget to drag and drop your conda environment into the workflow. Your environment name may be different depending on your setup. :::