PhasingNewHiC

Introduction

After deriving the haplotype using HaploC from a Hi-C dataset, this haplotype information can be directly applied to generate phased Hi-C maps from a new Hi-C dataset, provided it shares the same haplotype information. For instance, in a treatment vs. control experiment, the haplotype derived from the control's Hi-C dataset can be employed to produce phased Hi-C maps for the treatment's Hi-C dataset. This approach leverages existing haplotype data to facilitate the analysis of new datasets within the same experimental context.

Usage

Phasing new Hi-C data using pre-existing haplotypes involves all steps of HaploC, except SNP calling and haplotype inference. This can be summarized in three steps.

1. Create new_hic Folder: Set up a folder named 'new_hic' with the configuration file and fastq files.
2. Link to phased_hic: Establish a soft link from the SNP and haplotype folder in 'phased_hic' to the 'new_hic' folder.
3. Run HaploC Steps: Execute all HaploC steps, omitting SNP calling and haplotype inference.

We provide a one-line command for this process:

phasing_new_hic_slurm.sh -d $wk_dir -p $phased_dir ## slurm version
phasing_new_hic_cpu.sh -d $wk_dir -p $phased_dir ## cpu version

Examples

phasing_new_hic_slurm.sh -d demo_data_new -p demo_data ## slurm version
phasing_new_hic_cpu.sh -d demo_data_new -p demo_data ## cpu version

Output Structure

The output structure is the same as generated by running haploc_slurm.sh