The qBED track: a novel genome browser visualization for point processes

BioRxiv : the Preprint Server for Biology
A. MoudgilRobi David Mitra

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 CADD scores and GWAS hits, and 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 50.3.6. 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). We have also released a tutorial on how to upload qBED data to the browser (dx.doi.org/10.17504/protocols.io.bca8ishw).

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