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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, a technique used to investigate the three-dimensional organisation of a genome. The pipeline maps data to a specified reference genome and removes artefacts that would otherwise hinder subsequent analysis. HiCUP also provides an easy-to-interpret yet detailed quality control report that may be used by researchers to refine their experimental protocol for future studies. The software is freely available and has already been used for processing Hi-C data in several recently published peer-reviewed research articles. This experiment investigates the impact of using HiCUP to remove putative PCR amplification products in heavily duplicated Capture Hi-C libraries.

ORGANISM(S): Mus musculus

PROVIDER: GSE73204 | GEO | 2015/10/29

SECONDARY ACCESSION(S): PRJNA296367

REPOSITORIES: GEO

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HiCUP: pipeline for mapping and processing Hi-C data

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