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HaploC-tools user manual

Haplotype-specific Chromatin Conformation analysis tools contain a collection of modules to

1. Derive whole-chromosome haplotype from chromosome conformation capture (Hi-C) experiments (HaploC)
2. Generate unphased and phased (i.e., haplotype-specific) Hi-C maps (HaploC) and phasingNewHiC
3. Infer haplotype-resolved copy number status (HaploCNV)
4. Compare chromatin insulation between homologous chromosomes (HaploCI)
5. Compare compartment organization between homologous chromosomes (HaploCalder)
6. Phase any other type of sequencing data derived from the same individual (e.g., ChiP-Seq, RNA-seq, Repli-Seq etc.) for downstream allelic-specific analyses (phasingBam)

Follow the steps below to get started:

• Installation
• Prepare-working-directory
• Run HaploC-tools with slurm
• Run HaploC-tools without slurm
• Downstream-analysis

Demo data to test the tools can be downloaded from https://zenodo.org/records/10446020/files/demo_data.tar.gz?download=1