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

View ORCID ProfileArnav Moudgil, Daofeng Li, Silas Hsu, Deepak Purushotham, Ting Wang, View ORCID ProfileRobi David Mitra
doi: https://doi.org/10.1101/2020.04.27.060061
Arnav Moudgil
Washington University in St. Louis
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  • ORCID record for Arnav Moudgil
  • For correspondence: amoudgil@wustl.edu
Daofeng Li
Washington University in St. Louis
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  • For correspondence: dli23@wustl.edu
Silas Hsu
Washington University in St. Louis
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  • For correspondence: hsu.silas@wustl.edu
Deepak Purushotham
Washington University in St. Louis
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  • For correspondence: dpurushotham@wustl.edu
Ting Wang
Washington University in St. Louis
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  • For correspondence: twang@wustl.edu
Robi David Mitra
Washington University in St. Louis
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  • ORCID record for Robi David Mitra
  • For correspondence: rmitra@wustl.edu
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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).

Competing Interest Statement

The authors have declared no competing interest.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted April 29, 2020.
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The qBED track: a novel genome browser visualization for point processes
Arnav Moudgil, Daofeng Li, Silas Hsu, Deepak Purushotham, Ting Wang, Robi David Mitra
bioRxiv 2020.04.27.060061; doi: https://doi.org/10.1101/2020.04.27.060061
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The qBED track: a novel genome browser visualization for point processes
Arnav Moudgil, Daofeng Li, Silas Hsu, Deepak Purushotham, Ting Wang, Robi David Mitra
bioRxiv 2020.04.27.060061; doi: https://doi.org/10.1101/2020.04.27.060061

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