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bioRxiv · 10.1101/2020.04.27.060061

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

Moudgil, A.·Li, D.·Hsu, S.·Purushotham, D.·Wang, T.·Mitra, R. D.
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Abstract

SummaryTransposon 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/eQTL hits, and may have broad utility to the genomics community. Availability and ImplementationThe 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). 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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Moudgil, A., Li, D., Hsu, S., Purushotham, D., Wang, T., Mitra, R. D.. 2020-04-29. The qBED track: a novel genome browser visualization for point processes. https://doi.org/10.1101/2020.04.27.060061

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