runhic 0.6.3

A easy-to-use Hi-C processing software based on hiclib

Introduction

runHiC is a easy-to-use Hi-C processing software based on hiclib (https://bitbucket.org/mirnylab/hiclib) Different from hiclib, which was born for flexibility, runHiC is a customized pipeline, and can be run from command line directly.

Links

• Repository

• PyPI

Installation

Please check the file “INSTALL.rst” in the distribution.

Design Concepts

runHiC is able to perform the entire analysis from sequencing data to corrected contact matrices. It separates the whole process into 4 stages(mapping, filtering, binning, correcting). You can begin and end at any stage using certain subcommands.

7 subcommands are available:

mapping:

Iteratively map pair-end sequencing reads to a supplied genome

filtering:

Remove noises at the level of aligned read pairs and restriction fragments

binning:

Generate original contact matrices

correcting:

Perform iterative corrections on original contact matrices

tosparse:

Convert intra-chromosomal contact matrices to sparse ones

pileup:

Streamline all stages from mapping to correcting

quality:

Assess the quality of your experiments

visualize:

Plot the heatmap for given interval

Preparation

Please refer to the Sample folder distributed with our source code.

Directory Rearrangements

Although not required, I recommend creating a data root directory separate from the working directory.

Data Placement

Both genome and sequencing data should be placed under the data root directory.

Genome sequences should be stored chromosome by chromosome in FASTA format under a subfolder(named after corresponding genome name).

Sequencing read-pairs should be stored in SRA or FASTQ format under another subfolder(any valid name).

Meta Data

Construct a meta data file describing your sequencing data under the working directory

Four columns are required: prefix of SRA file name, cell line name, biological replicate label, and restriction enzyme name. An example file(Sample/working/datasets.tsv) is distributed along with this software, please check it.

Usage

Open a terminal, type runHiC -h and runHiC <subcommand> -h for help information.