ChIA-DropBox: a novel analysis and visualization pipeline for multiplex chromatin interactions-


ChIA-DropBox: a novel analysis and visualization pipeline for multiplex chromatin interactions

发布日期:2019-02-28 发表者:肖尚桃 浏览次数:次

报告人:Dr. Zhongyuan Tian



摘要:ChIA-Drop is a new experimental technique for mapping multiplex chromatin interactions with single-molecule precision via droplet-based and barcode-linked sequencing. Here, we developed a custom pipeline, called ChIA-DropBox, for processing and visualizing ChIA-Drop data. First, ChIA-DropBox maps sequencing reads, selects high-quality reads, and identifies each read’s barcode from its droplet of origin. Then, ChIA-DropBox groups together reads with the same barcode, and calls statistically significant chromatin complexes via a resampling-based approach to assess domain-based interaction frequencies. ChIA-DropBox also includes an interactive visualization tool, called ChIA-view, for viewing multiplex chromatin complexes. In ChIA-view, the fragments in each chromatin complex are displayed in their genomic alignments along the x-axis, and the different chromatin complexes are arranged by similarity along the y-axis via hierarchical clustering. Notably, ChIA-view can be generalized to any multiplex chromatin interaction data. The visualization tool in ChIA-DropBox also prepares the ChIA-Drop mapping data for 2D contact views in Juicebox. ChIA-DropBox has been successfully applied to ChIA-Drop datasets of various sequencing depths and in multiple species, demonstrating the pipeline’s reliability, versatility, and scalability.

报告人简介:Dr. Zhongyuan Tian got his Ph.D from Yamaguchi University in Japan. Currently, he is working at The Jackson Laboratory for Genomic Medicine (Connecticut, U.S.) as Postdoctoral Associate. He is focusing on pipeline development for 3D novel technology, and has developed ChIA-DropBox for ChIA-Drop data analysis and visualization. He also contributes to data processing and data analysis for protein-RNA-chromatin interactions.