nested-TAD-detection

To detect nested TADs from Hi-C data, provide your .mcool file path, target chromosome, and resolution. The skill extracts a dense matrix and runs OnTAD to identify hierarchical TADs and sub-TADs, generating BED-like outputs.

Yes, hierarchical TAD calling supports .mcool, .cool, and .hic Hi-C inputs. You specify the chromosome and resolution to extract a dense matrix, then OnTAD annotates the nested TAD structures and produces standardized BED-like outputs.

The best way to extract a dense matrix for OnTAD is by supplying the Hi-C file path, chromosome name, and resolution. This skill handles the extraction from multi-resolution cooler files, preparing the input required for nested TAD detection.

Yes, an environment with cooler and OnTAD tooling is required. The process depends on cooler to extract dense matrices from your Hi-C files before OnTAD runs the hierarchical TAD annotation and generates the final BED-like output files.

When identifying nested TAD boundaries, OnTAD generates organized BED-like files and annotation outputs. These standardized results detail the hierarchical TAD and sub-TAD boundaries, enabling direct integration with downstream regulatory feature analyses.

Nested TAD detection across multi-resolution Hi-C data requires selecting a single chromosome and resolution per run. The skill validates matrix quality before running OnTAD, but processing is constrained to chromosome-specific analyses rather than whole-genome batches.