HaploCalder

Introduction

HaploCalder detects significant differences in chromatin compartment organization between the two haplotypes. It is a custom version of CALDER2, see CALDER2 for more details about sub-compartment calling.

HaploCalder contains three main steps:

1. Region selection for compartment inference
2. Bin size selection
3. Differential compartment calls

Usage

HaploC-tools/bin/downstreams.sh --help

Examples

conda run -n nHapCUT2 HaploC-tools/bin/downstreams.sh -d demo_data -k diffComp

Parameters:

Name	Description
-d	The working directory for phasing
-k	The module to run, should be one of diffIns, diffComp or HaploCNV

Output Structure

The output of the workflow is stored in the CALDER/diffComp sub-directory and will look like this:

CALDER/diffComp/
|-- diffComp.sig.bed
|-- diffComp.sig.wig
|-- phased.diff_rank.bedgraph
|-- random_k=1.diff_rank.bedgraph
|-- random_k=2.diff_rank.bedgraph
|-- random_k=3.diff_rank.bedgraph
|-- random_k=4.diff_rank.bedgraph
`-- random_k=5.diff_rank.bedgraph

File description:

Name	Description
diffComp.sig.bed	a .bed file containing the genomic regions showing significant compartment difference between the two haplotypes
diffComp.sig.wig	a .wig file containing the magnitude of compartment differences
phased.diff_rank.bedgraph	a .bedgraph file containing the difference of compartment rank at each 10kb bin between 'pat' and 'mat' Hi-C map
random_k=xx.diff_rank.bedgraph	a .bedgraph file containing the difference of compartment rank at each 10kb bin between two random (pseudo) 'pat' and 'mat' Hi-C map

All .bedgraph and .wig files can be viewed directly through IGV, as exemplified here: