JinLabBioinfo / HiCorr

HiCorr: a Hi-C data bias-correction pipeline

HiCorr

HiCorr is a pipeline designed to do bias-correction and visualization for multi-platform Hi-C(in-situ Hi-C, Arima, micro-C). HiCorr focuses on the mapping of chromatin interactions at high-resolution, especially the sub-TAD ~5kb resolution enhancer-promoter interactions, which requires more rigorous bias-correction. It needs to be run in an unix/linux environment. Currently it includes reference files of genome build hg19 and mm10, the reference files for other genome build will be provided upon request, please contact Shanshan Zhang([e-mail]) or Fulai Jin([e-mail]). For a noise-free and enhanced signal, please check DeepLoop we recently developed.

Setup

git clone https://github.com/shanshan950/HiCorr.git
cd HiCorr/
chmod 755 HiCorr
chmod -R 755 bin/*

Gateway for different Hi-C data type:

Each section descibes reference file downloading, preprocessing (mapping and fragment filteration), and how to run HiCorr.

👉 HiCorr on micro-C (beta version)

👉 HiCorr on Arima (beta version)

👉 HiCorr on HindIII enzyme Hi-C

👉 HiCorr on eHi-C

👉 HiCorr on in-situ Hi-C or DPNII/Mbol enzyme Hi-C

👉 Visualize HiCorr contact heatmaps

👉 Compatible with HiCPro valid pairs

👉 Generate reference files for HiCorr

👀 40 Processed Hi-C datasets by HiCorr and DeepLoop can be visualized in website

Citation:

Lu,L. et al. Robust Hi-C Maps of Enhancer-Promoter Interactions Reveal the Function of Non-coding Genome in Neural Development and Diseases. Molecular Cell; doi: https://doi.org/10.1016/j.molcel.2020.06.007