hic-tad-calling

To identify TADs from .mcool or .cool files, this skill automates TAD boundary calling using HiCExplorer and overlays the results on contact maps for your specified genomic regions. You simply provide the sample name, file path, target genome assembly, and resolution to generate the visualizations.

TAD calling is the automated identification of topologically associating domain boundaries from Hi-C contact matrices. This skill uses HiCExplorer to delineate these domains from your input data, enabling region-specific analysis and interpretability of genome organization.

Yes, you can use .hic files for TAD calling and visualization. The skill supports Hi-C data stored in .mcool, .cool, or .hic formats, requiring you to specify a genome assembly, resolution, and target genomic regions to guide the workflow.

To start automated TAD calling with HiCExplorer, you need your Hi-C data in .mcool, .cool, or .hic format, a chosen genome assembly, and specified target genomic regions. Providing the sample name and file path initiates the boundary identification and visualization process.

Yes, this TAD calling workflow supports region-specific analyses by allowing you to specify target genomic regions. It generates contact maps with TAD boundaries overlaid exactly on those user-specified genome loci for focused interpretation.

Specifying resolution is required to guide the TAD calling workflow on Hi-C contact maps stored in .mcool or .cool files. The chosen resolution directly impacts the automated identification of TAD boundaries and the resulting visualization of genome organization.