Abstract

Summary

Transposon calling cards is a genomic assay for identifying transcription factor binding sites in both bulk and single cell experiments. Here, we describe the qBED format, an open, text-based standard for encoding and analyzing calling card data. In parallel, we introduce the qBED track on the WashU Epigenome Browser, a novel visualization that enables researchers to inspect calling card data in their genomic context. Finally, through examples, we demonstrate that qBED files can be used to visualize non-calling card datasets, such as Combined Annotation-Dependent Depletion scores and GWAS/eQTL hits, and thus may have broad utility to the genomics community.

Availability and implementation

The qBED track is available on the WashU Epigenome Browser (http://epigenomegateway.wustl.edu/browser), beginning with version 46. Source code for the WashU Epigenome Browser with qBED support is available on GitHub (http://github.com/arnavm/eg-react and http://github.com/lidaof/eg-react). A complete definition of the qBED format is available as part of the WashU Epigenome Browser documentation (https://eg.readthedocs.io/en/latest/tracks.html#qbed-track). We have also released a tutorial on how to upload qBED data to the browser (http://dx.doi.org/10.17504/protocols.io.bca8ishw).

中文翻译：

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qBED track：一种用于点过程的新型基因组浏览器可视化

摘要

概括

转座子名片是一种基因组分析，用于在大量和单细胞实验中识别转录因子结合位点。在这里，我们描述了 qBED 格式，这是一种用于编码和分析电话卡数据的基于文本的开放标准。同时，我们在 WashU Epigenome Browser 上引入了 qBED track，这是一种新颖的可视化，使研究人员能够在其基因组环境中检查名片数据。最后，通过示例，我们证明 qBED 文件可用于可视化非名片数据集，例如 Combined Annotation-Dependent Depletion 分数和 GWAS/eQTL 命中，因此可能对基因组学社区具有广泛的实用性。

可用性和实施

qBED 轨道可在 WashU 表观基因组浏览器 (http://epigenomegateway.wustl.edu/browser) 上获得，从版本 46 开始。具有 qBED 支持的 WashU 表观基因组浏览器的源代码可在 GitHub (http://github. com/arnavm/eg-react 和 http://github.com/lidaof/eg-react）。qBED 格式的完整定义可作为 WashU Epigenome Browser 文档的一部分 (https://eg.readthedocs.io/en/latest/tracks.html#qbed-track)。我们还发布了如何将 qBED 数据上传到浏览器的教程 (http://dx.doi.org/10.17504/protocols.io.bca8ishw)。