Software tools for visualizing Hi-C data

Galip Gürkan Yardimci; William Stafford Noble

doi:10.1186/s13059-017-1161-y

Software tools for visualizing Hi-C data

Galip Gürkan Yardimci, William Stafford Noble

Research output: Contribution to journal › Review article › peer-review

45 Scopus citations

Abstract

High-throughput assays for measuring the three-dimensional (3D) configuration of DNA have provided unprecedented insights into the relationship between DNA 3D configuration and function. Data interpretation from assays such as ChIA-PET and Hi-C is challenging because the data is large and cannot be easily rendered using standard genome browsers. An effective Hi-C visualization tool must provide several visualization modes and be capable of viewing the data in conjunction with existing, complementary data. We review five software tools that do not require programming expertise. We summarize their complementary functionalities, and highlight which tool is best equipped for specific tasks.

Original language	English (US)
Article number	26
Journal	Genome biology
Volume	18
Issue number	1
DOIs	https://doi.org/10.1186/s13059-017-1161-y
State	Published - Feb 3 2017
Externally published	Yes

ASJC Scopus subject areas

Ecology, Evolution, Behavior and Systematics
Genetics
Cell Biology

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10.1186/s13059-017-1161-y

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AB - High-throughput assays for measuring the three-dimensional (3D) configuration of DNA have provided unprecedented insights into the relationship between DNA 3D configuration and function. Data interpretation from assays such as ChIA-PET and Hi-C is challenging because the data is large and cannot be easily rendered using standard genome browsers. An effective Hi-C visualization tool must provide several visualization modes and be capable of viewing the data in conjunction with existing, complementary data. We review five software tools that do not require programming expertise. We summarize their complementary functionalities, and highlight which tool is best equipped for specific tasks.

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Software tools for visualizing Hi-C data

Abstract

ASJC Scopus subject areas

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