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.
Please check the file "INSTALL.rst" in the distribution.
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 |
Please refer to the Sample folder distributed with our source code.
Although not required, I recommend creating a data root directory separate from the working directory.
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).
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.
Open a terminal, type runHiC -h and runHiC <subcommand> -h for help information.
Xiaotao Wang. (2016). runHiC: A user-friendly Hi-C data processing software based on hiclib. Zenodo. 10.5281/zenodo.55324