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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 D. Mitra
doi: https://doi.org/10.1101/2020.04.27.060061
Arnav Moudgil
1Department of Genetics, Washington University in St. Louis School of Medicine, St. Louis MO 63110, USA
2Edison Family Center for Genome Sciences and Systems Biology, Washington University in St. Louis School of Medicine, St. Louis MO 63110, USA
3Medical Scientist Training Program, Washington University in St. Louis School of Medicine, St. Louis MO 63110, USA
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  • ORCID record for Arnav Moudgil
Daofeng Li
1Department of Genetics, Washington University in St. Louis School of Medicine, St. Louis MO 63110, USA
2Edison Family Center for Genome Sciences and Systems Biology, Washington University in St. Louis School of Medicine, St. Louis MO 63110, USA
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Silas Hsu
1Department of Genetics, Washington University in St. Louis School of Medicine, St. Louis MO 63110, USA
2Edison Family Center for Genome Sciences and Systems Biology, Washington University in St. Louis School of Medicine, St. Louis MO 63110, USA
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Deepak Purushotham
1Department of Genetics, Washington University in St. Louis School of Medicine, St. Louis MO 63110, USA
2Edison Family Center for Genome Sciences and Systems Biology, Washington University in St. Louis School of Medicine, St. Louis MO 63110, USA
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Ting Wang
1Department of Genetics, Washington University in St. Louis School of Medicine, St. Louis MO 63110, USA
2Edison Family Center for Genome Sciences and Systems Biology, Washington University in St. Louis School of Medicine, St. Louis MO 63110, USA
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Robi D. Mitra
1Department of Genetics, Washington University in St. Louis School of Medicine, St. Louis MO 63110, USA
2Edison Family Center for Genome Sciences and Systems Biology, Washington University in St. Louis School of Medicine, St. Louis MO 63110, USA
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  • ORCID record for Robi D. 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/eQTL 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 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).

Competing Interest Statement

The authors have declared no competing interest.

Footnotes

  • Edited text for clarity.

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 30, 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 D. 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 D. Mitra
bioRxiv 2020.04.27.060061; doi: https://doi.org/10.1101/2020.04.27.060061

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