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ChIA-PIPE: A fully automated pipeline for ChIA-PET data analysis and visualization

Daniel Capurso, Jiahui Wang, Simon Zhongyuan Tian, Liuyang Cai, Sandeep Namburi, Byoungkoo Lee, Harianto Tjong, Zhonghui Tang, Ping Wang, Chia-Lin Wei, Yijun Ruan, Sheng Li
doi: https://doi.org/10.1101/506683
Daniel Capurso
1The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut, USA
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Jiahui Wang
1The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut, USA
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Simon Zhongyuan Tian
1The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut, USA
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Liuyang Cai
1The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut, USA
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Sandeep Namburi
1The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut, USA
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Byoungkoo Lee
1The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut, USA
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Harianto Tjong
1The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut, USA
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Zhonghui Tang
1The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut, USA
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Ping Wang
1The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut, USA
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Chia-Lin Wei
1The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut, USA
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  • For correspondence: chia-lin.wei@jax.org yijun.ruan@jax.org sheng.li@jax.org
Yijun Ruan
1The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut, USA
2Department of Genetics and Genome Sciences, University of Connecticut Health Center, Farmington, Connecticut, USA
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  • For correspondence: chia-lin.wei@jax.org yijun.ruan@jax.org sheng.li@jax.org
Sheng Li
1The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut, USA
2Department of Genetics and Genome Sciences, University of Connecticut Health Center, Farmington, Connecticut, USA
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  • For correspondence: chia-lin.wei@jax.org yijun.ruan@jax.org sheng.li@jax.org
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Abstract

ChIA-PET enables the genome-wide discovery of chromatin interactions involving specific protein factors, with base-pair resolution. Interpreting ChIA-PET data depends on having a robust analytic pipeline. Here, we introduce ChIA-PIPE, a fully automated pipeline for ChIA-PET data processing, quality assessment, analysis, and visualization. ChIA-PIPE performs linker filtering, read mapping, peak calling, loop calling, chromatin-contact-domain calling, and can resolve allele-specific peaks and loops. ChIA-PIPE also automates quality-control assessment for each dataset. Furthermore, ChIA-PIPE generates input files for visualizing 2D contact maps with Juicebox and HiGlass, and provides a new dockerized visualization tool for high-resolution, browser-based exploration of peaks and loops. With minimal adjusting, ChIA-PIPE can also be suited for the analysis of other related chromatin-mapping data.

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Posted December 27, 2018.
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ChIA-PIPE: A fully automated pipeline for ChIA-PET data analysis and visualization
Daniel Capurso, Jiahui Wang, Simon Zhongyuan Tian, Liuyang Cai, Sandeep Namburi, Byoungkoo Lee, Harianto Tjong, Zhonghui Tang, Ping Wang, Chia-Lin Wei, Yijun Ruan, Sheng Li
bioRxiv 506683; doi: https://doi.org/10.1101/506683
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ChIA-PIPE: A fully automated pipeline for ChIA-PET data analysis and visualization
Daniel Capurso, Jiahui Wang, Simon Zhongyuan Tian, Liuyang Cai, Sandeep Namburi, Byoungkoo Lee, Harianto Tjong, Zhonghui Tang, Ping Wang, Chia-Lin Wei, Yijun Ruan, Sheng Li
bioRxiv 506683; doi: https://doi.org/10.1101/506683

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