HaploHiC

Comprehensive haplotype division of Hi-C PE-reads based on local contacts ratio.

• Author: Wenlong Jia
• Email: wenlongkxm@gmail.com

Version

0.34

Installation

HaploHiC is written in PERL. All of its functions are packaged into a standalone PERL module. Besides, it also requires other additional modules.

To install HaploHiC, you need to download HaploHiC and add the current directory to the PERL5LIB path.

git clone https://github.com/Nobel-Justin/HaploHiC.git
PERL5LIB=$PERL5LIB:$PWD; export PERL5LIB

List of additional PERL modules required:

• JSON
• SVG
• Parallel::ForkManager
• List::Util
• BioFuse

If you encounter problems, please open an issue at the project on Github.

Usage

HaploHiC provides series of commands for Hi-C data analysis.

Usage:   perl HaploHiC.pl <command>

Commands:

-- Haplotype work
   haplo_div      divide the diploid haplotype (P/M) Hi-C reads from alignment.
   plotLocReg     plot phased local region information.

-- Extensions
   juicer_db      make database files for juicer and HaploHiC operations.
   juicerDump     run juicer dump, and merge the inter-chr and intra-chr.
   FRAG_gene      convert FRAG contacts to gene level contacts.

Haplotype work

• haplo_div

  haplo_div loads alignment file(s) of Hi-C data and haplotype information, and assigns haplotypes to Hi-C PE-reads of unknown parental origin according to contacts information (local contacts ratio) in local genomic regions with dynamic size. Please check the demo.

• plotLocReg

  plotLocReg loads statistics generated by haplo_div to plot information of phased local region which calculates the local contacts ratio.

Extensions

• juicer_db

  juicer_db automatically prepares database files. This database supports operation of both juicer and HaploHiC. Please check the demo.

• juicerDump

  juicerDump runs juicer dump on each pairwise inter/intra-chr chromosomes, and merge the results.

• FRAG_gene

  FRAG_gene loads contact matrix of FRAG level, and outputs the GENE level contacts.