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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.

SUBMITTER: Wingett S 

PROVIDER: S-EPMC4706059 | biostudies-literature | 2015

REPOSITORIES: biostudies-literature

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HiCUP: pipeline for mapping and processing Hi-C data.

Wingett Steven S   Ewels Philip P   Furlan-Magaril Mayra M   Nagano Takashi T   Schoenfelder Stefan S   Fraser Peter P   Andrews Simon S  

F1000Research 20151120


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 h  ...[more]

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