Journal
BIOINFORMATICS
Volume 37, Issue 8, Pages 1168-1170Publisher
OXFORD UNIV PRESS
DOI: 10.1093/bioinformatics/btaa771
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Funding
- National Institutes of Health [F30 HG009986, RF1 MH117070, R01 GM123203, R01 HG007354, R01 HG007175, R01 ES024992, U01 CA200060, U24 ES026699, U01 HG009391]
- American Cancer Society [RSG-14-049-01-DMC]
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Transposon calling cards is a genomic assay used to identify transcription factor binding sites, and qBED format is an open standard for encoding and analyzing calling card data. The qBED track on the WashU Epigenome Browser allows researchers to visualize calling card data in their genomic context. Through examples, it has been shown that qBED files can also be used to visualize non-calling card datasets, indicating potential broad utility to the genomics community.
A 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 Combined Annotation-Dependent Depletion scores and GWAS/eQTL hits, and thus may have broad utility to the genomics community.
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