ChIA-PIPE: A fully automated pipeline for comprehensive ChIA-PET data analysis and visualization
| العنوان: | ChIA-PIPE: A fully automated pipeline for comprehensive ChIA-PET data analysis and visualization |
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| المؤلفون: | Byoungkoo Lee, Ping Wang, Yijun Ruan, Chia-Lin Wei, Ahmed Abbas, Zhonghui Tang, Jiahui Wang, Sandeep Namburi, Liuyang Cai, Minji Kim, Harianto Tjong, Yuliang Feng, Sheng Li |
| المصدر: | Science Advances |
| بيانات النشر: | American Association for the Advancement of Science (AAAS), 2020. |
| سنة النشر: | 2020 |
| مصطلحات موضوعية: | 0303 health sciences, Loop (graph theory), Data processing, Multidisciplinary, genetic structures, Computer science, Systems Biology, education, SciAdv r-articles, computer.software_genre, Data type, Pipeline (software), Chromatin, Visualization, 03 medical and health sciences, 0302 clinical medicine, Data mining, Peak calling, computer, Research Articles, 030217 neurology & neurosurgery, ChIA-PET, Research Article, 030304 developmental biology |
| الوصف: | New genome pipeline enables seamless execution of processing, analyzing, and visualizing of ChIA-PET data. ChIA-PET (chromatin interaction analysis with paired-end tags) enables genome-wide discovery of chromatin interactions involving specific protein factors, with base pair resolution. Interpretation of ChIA-PET data requires a robust analytic pipeline. Here, we introduce ChIA-PIPE, a fully automated pipeline for ChIA-PET data processing, quality assessment, visualization, and analysis. ChIA-PIPE performs linker filtering, read mapping, peak calling, and loop calling and automates quality control assessment for each dataset. To enable visualization, ChIA-PIPE generates input files for two-dimensional contact map viewing with Juicebox and HiGlass and provides a new dockerized visualization tool for high-resolution, browser-based exploration of peaks and loops. To enable structural interpretation, ChIA-PIPE calls chromatin contact domains, resolves allele-specific peaks and loops, and annotates enhancer-promoter loops. ChIA-PIPE also supports the analysis of other related chromatin-mapping data types. |
| تدمد: | 2375-2548 |
| URL الوصول: | https://explore.openaire.eu/search/publication?articleId=doi_dedup___::3fe26baa745ea697ed3b0c4f382c5ece https://doi.org/10.1126/sciadv.aay2078 |
| حقوق: | OPEN |
| رقم الأكسشن: | edsair.doi.dedup.....3fe26baa745ea697ed3b0c4f382c5ece |
| قاعدة البيانات: | OpenAIRE |
| تدمد: | 23752548 |
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