ChIA-PET tool for comprehensive chromatin interaction analysis with paired-end tag sequencing

Guoliang Li; Melissa J. Fullwood; Han Xu; Fabianus Hendriyan Mulawadi; Stoyan Velkov; Vinsensius Vega; Pramila Nuwantha Ariyaratne; Yusoff Bin Mohamed; Hong Sain Ooi; Chandana Tennakoon; Chia Lin Wei; Yijun Ruan; Wing Kin Sung

doi:10.1186/gb-2010-11-2-r22

ChIA-PET tool for comprehensive chromatin interaction analysis with paired-end tag sequencing

Guoliang Li, Melissa J. Fullwood, Han Xu, Fabianus Hendriyan Mulawadi, Stoyan Velkov, Vinsensius Vega, Pramila Nuwantha Ariyaratne, Yusoff Bin Mohamed, Hong Sain Ooi, Chandana Tennakoon, Chia Lin Wei, Yijun Ruan, Wing Kin Sung

Research output: Contribution to journal › Article › peer-review

225 Scopus citations

Abstract

Chromatin interaction analysis with paired-end tag sequencing (ChIA-PET) is a new technology to study genome-wide long-range chromatin interactions bound by protein factors. Here we present ChIA-PET Tool, a software package for automatic processing of ChIA-PET sequence data, including linker filtering, mapping tags to reference genomes, identifying protein binding sites and chromatin interactions, and displaying the results on a graphical genome browser. ChIA-PET Tool is fast, accurate, comprehensive, user-friendly, and open source.

Original language	English (US)
Article number	r22
Journal	Genome biology
Volume	11
Issue number	2
DOIs	https://doi.org/10.1186/gb-2010-11-2-r22
State	Published - Feb 25 2010
Externally published	Yes

ASJC Scopus subject areas

Ecology, Evolution, Behavior and Systematics
Genetics
Cell Biology

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10.1186/gb-2010-11-2-r22

Cite this

@article{5747ee7fbc224060b0cdca52c8b820bf,

title = "ChIA-PET tool for comprehensive chromatin interaction analysis with paired-end tag sequencing",

abstract = "Chromatin interaction analysis with paired-end tag sequencing (ChIA-PET) is a new technology to study genome-wide long-range chromatin interactions bound by protein factors. Here we present ChIA-PET Tool, a software package for automatic processing of ChIA-PET sequence data, including linker filtering, mapping tags to reference genomes, identifying protein binding sites and chromatin interactions, and displaying the results on a graphical genome browser. ChIA-PET Tool is fast, accurate, comprehensive, user-friendly, and open source.",

author = "Guoliang Li and Fullwood, {Melissa J.} and Han Xu and Mulawadi, {Fabianus Hendriyan} and Stoyan Velkov and Vinsensius Vega and Ariyaratne, {Pramila Nuwantha} and Mohamed, {Yusoff Bin} and Ooi, {Hong Sain} and Chandana Tennakoon and Wei, {Chia Lin} and Yijun Ruan and Sung, {Wing Kin}",

note = "Funding Information: The authors thank the anonymous reviewers for their valuable comments. We acknowledge the Genome Technology and Biology Group at the Genome Institute of Singapore for technical support; Mr Atif Shahab and Mr Chan Chee Seng for computing support. GL is supported by a GIS post-doctoral fellowship. MJF is supported by an A*STAR scholarship and a L'Oreal-UNESCO For Women In Science National Fellowship. YR and C-L W are supported by A*STAR of Singapore and NIH ENCODE grants (R01 HG004456-01, R01HG003521-01, and part of 1U54HG004557-01).",

year = "2010",

month = feb,

day = "25",

doi = "10.1186/gb-2010-11-2-r22",

language = "English (US)",

volume = "11",

journal = "Genome biology",

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TY - JOUR

T1 - ChIA-PET tool for comprehensive chromatin interaction analysis with paired-end tag sequencing

AU - Li, Guoliang

AU - Fullwood, Melissa J.

AU - Xu, Han

AU - Mulawadi, Fabianus Hendriyan

AU - Velkov, Stoyan

AU - Vega, Vinsensius

AU - Ariyaratne, Pramila Nuwantha

AU - Mohamed, Yusoff Bin

AU - Ooi, Hong Sain

AU - Tennakoon, Chandana

AU - Wei, Chia Lin

AU - Ruan, Yijun

AU - Sung, Wing Kin

N1 - Funding Information: The authors thank the anonymous reviewers for their valuable comments. We acknowledge the Genome Technology and Biology Group at the Genome Institute of Singapore for technical support; Mr Atif Shahab and Mr Chan Chee Seng for computing support. GL is supported by a GIS post-doctoral fellowship. MJF is supported by an A*STAR scholarship and a L'Oreal-UNESCO For Women In Science National Fellowship. YR and C-L W are supported by A*STAR of Singapore and NIH ENCODE grants (R01 HG004456-01, R01HG003521-01, and part of 1U54HG004557-01).

PY - 2010/2/25

Y1 - 2010/2/25

N2 - Chromatin interaction analysis with paired-end tag sequencing (ChIA-PET) is a new technology to study genome-wide long-range chromatin interactions bound by protein factors. Here we present ChIA-PET Tool, a software package for automatic processing of ChIA-PET sequence data, including linker filtering, mapping tags to reference genomes, identifying protein binding sites and chromatin interactions, and displaying the results on a graphical genome browser. ChIA-PET Tool is fast, accurate, comprehensive, user-friendly, and open source.

AB - Chromatin interaction analysis with paired-end tag sequencing (ChIA-PET) is a new technology to study genome-wide long-range chromatin interactions bound by protein factors. Here we present ChIA-PET Tool, a software package for automatic processing of ChIA-PET sequence data, including linker filtering, mapping tags to reference genomes, identifying protein binding sites and chromatin interactions, and displaying the results on a graphical genome browser. ChIA-PET Tool is fast, accurate, comprehensive, user-friendly, and open source.

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DO - 10.1186/gb-2010-11-2-r22

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VL - 11

JO - Genome biology

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IS - 2

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ER -

ChIA-PET tool for comprehensive chromatin interaction analysis with paired-end tag sequencing

Abstract

ASJC Scopus subject areas

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