HiCUP: pipeline for mapping and processing Hi-C data

By Steven W. Wingett, Philip A. Ewels, Mayra Furlan-Magaril, Takashi Nagano, Stefan Schoenfelder, Peter Fraser, Simon R. Andrews. F1000Research, 2015

695 citations recorded by the source corpus.

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.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/c053276e963a56036b8e93d42195af5aad6f836b

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In Molecular Biology

1. J. Peters
2. Peter Fraser
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4. Roman R. Stocsits

Citations in the corpus

• Topologically associating domains and chromatin loops depend on cohesin and are regulated by CTCF, WAPL, and PDS5 proteins (2017, methodology): “Hi-C data processing and normalization Raw sequencing reads were processed using the HiCUP pipeline (Wingett et al, 2015).”