![]() Li G., Fullwood M.J., Xu H., Mulawadi F.H., Velkov S., Vega V., Ariyaratne P.N., Mohamed Y.B., Ooi H.S., Tennakoon C., et al. Chromatin interaction analysis with paired-end tag (ChIA-PET) sequencing technology and application. Li G., Cai L., Chang H., Hong P., Zhou Q., Kulakova E.V., Ruan Y. An oestrogen-receptor-α-bound human chromatin interactome. ![]() The ChIA-PET Tool V3 is publicly available at GitHub.ĬhIA-PET chromatin interaction analysis with paired-end tag data analysis chromatin interactions genome-wide high-throughput.įullwood M.J., Liu M.H., Pan Y.F., Liu J., Xu H., Mohamed Y.B., Orlov Y.L., Velkov S., Ho A., Mei P.H., et al. There is higher enrichment for significant chromatin interactions from ChIA-PET Tool V3 in aggregate peak analysis (APA) plots. Most peaks detected by the ChIA-PET Tool V3 overlap with those of other tools. We compared our tool with existing tools, including ChiaSig, MICC, Mango and ChIA-PET2, by using the same public data set in the same computer. In this paper, we provide a detailed demonstration of the design of ChIA-PET Tool V3 and how to install it and analyze RNA polymerase II (RNAPII) ChIA-PET data from human K562 cells with it. It processes short-read and long-read ChIA-PET data with multithreading and generates statistics of results in an HTML file. Here, we present the updated version of ChIA-PET Tool (V3) as a computational package to process the next-generation sequence data generated from ChIA-PET experiments. We developed ChIA-PET Tool for ChIA-PET data analysis in 2010. Chromatin Interaction Analysis with Paired-End Tag (ChIA-PET) sequencing is a genome-wide high-throughput technology that detects chromatin interactions associated with a specific protein of interest. Understanding chromatin interactions is important because they create chromosome conformation and link the cis- and trans- regulatory elements to their target genes for transcriptional regulation.
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