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

Abstract

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. 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).