bio-workflows-hic-pipeline

To process Hi-C reads into A/B compartments and TAD boundaries, you need an end-to-end workflow handling alignment, matrix generation, and ICE balancing. This pipeline automates those steps to generate balanced matrices and detect higher-order genome features across resolutions.

Calling chromatin loops from cooler matrices requires applying cooltools for downstream analysis and visualization. This workflow provides compatible code snippets and example workflows to automate loop calling across multiple resolutions from balanced contact matrices.

Yes, cooltools works with cooler matrices for Hi-C compartment analysis. This workflow is compatible with both tools, enabling you to identify A/B compartments, TAD boundaries, and chromatin loops across various resolutions from the generated balanced matrices.

ICE balancing is required before detecting TADs and loops in Hi-C data to correct raw contact matrices. This pipeline includes the ICE balancing step as part of the end-to-end process, ensuring matrix quality before downstream compartment and TAD analysis.

An end-to-end Hi-C pipeline generates balanced matrices by automating alignment, contact matrix generation, and ICE balancing from raw reads. This workflow consolidates these preprocessing steps into a single reproducible process before identifying compartments and loops.

Running a complete Hi-C workflow requires cooler and cooltools for matrix handling and downstream analysis. This pipeline includes specific version requirements and tool dependencies aligned with these frameworks for preprocessing and feature detection.