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bioRxiv · 10.1101/506683

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

Capurso, D.·Wang, J.·Tian, S. Z.·Cai, L.·Namburi, S.·Lee, B.·Tjong, H.·Tang, Z.·Wang, P.·Wei, C.-L.·Ruan, Y.·Li, S.
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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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Capurso, D., Wang, J., Tian, S. Z., Cai, L., Namburi, S., Lee, B., Tjong, H., Tang, Z., Wang, P., Wei, C.-L., Ruan, Y., Li, S.. 2018-12-27. ChIA-PIPE: A fully automated pipeline for ChIA-PET data analysis and visualization. https://doi.org/10.1101/506683

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