HiCUP: pipeline for mapping and processing Hi-C data

Abstract

HiCUP is a pipeline for processing sequence data generated by Hi-C and Capture Hi-C (CHi-C) experiments, which are techniques used to investigate three-dimensional genomic organisation. The pipeline maps data to a specified reference genome and removes artefacts that would otherwise hinder subsequent analysis. HiCUP also produces an easy-to-interpret yet detailed quality control (QC) report that assists in refining experimental protocols for future studies. The software is freely available and has already been used for processing Hi-C and CHi-C data in several recently published peer-reviewed studies.

Cited by papers we hold 21

• A chromosome-level genome assembly and annotation of the maize elite breeding line Dan340 · 2022
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• Cohesin Disrupts Polycomb-Dependent Chromosome Interactions in Embryonic Stem Cells · 2020
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• PRC1 Catalytic Activity Is Central to Polycomb System Function · 2020
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• Galaxy HiCExplorer 3: a web server for reproducible Hi-C, capture Hi-C and single-cell Hi-C data analysis, quality control and visualization · 2020
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• RADICL-seq identifies general and cell type–specific principles of genome-wide RNA-chromatin interactions · 2020
  Corrected
• Emergence of the Ug99 lineage of the wheat stem rust pathogen through somatic hybridisation · 2019
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• An Overview of Methods for Reconstructing 3-D Chromosome and Genome Structures from Hi-C Data · 2019
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• p63 cooperates with CTCF to modulate chromatin architecture in skin keratinocytes · 2019
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• GenPipes: an open-source framework for distributed and scalable genomic analyses · 2019
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• A chromosome-scale genome assembly of cucumber ( Cucumis sativus L.) · 2019
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• The chromosome-scale reference genome of black pepper provides insight into piperine biosynthesis · 2019
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• Genome-scale Capture C promoter interactions implicate effector genes at GWAS loci for bone mineral density · 2019
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• Galaxy HiCExplorer: a web server for reproducible Hi-C data analysis, quality control and visualization · 2018
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• Genome organization and DNA accessibility control antigenic variation in trypanosomes · 2018
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• A promoter interaction map for cardiovascular disease genetics · 2018
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• Genome-wide association study of classical Hodgkin lymphoma identifies key regulators of disease susceptibility · 2017
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• Hi-C as a tool for precise detection and characterisation of chromosomal rearrangements and copy number variation in human tumours · 2017
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• Global reorganisation of cis-regulatory units upon lineage commitment of human embryonic stem cells · 2017
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• Lineage-Specific Genome Architecture Links Enhancers and Non-coding Disease Variants to Target Gene Promoters · 2016
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• CHiCAGO: robust detection of DNA looping interactions in Capture Hi-C data · 2016
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and 1 more

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