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Bedshift: perturbation of genomic interval sets

View ORCID ProfileAaron Gu, View ORCID ProfileHyun Jae Cho, View ORCID ProfileNathan C. Sheffield
doi: https://doi.org/10.1101/2020.11.11.378554
Aaron Gu
1Center for Public Health Genomics, University of Virginia
5Department of Computer Science, University of Virginia School of Engineering
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Hyun Jae Cho
1Center for Public Health Genomics, University of Virginia
5Department of Computer Science, University of Virginia School of Engineering
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Nathan C. Sheffield
1Center for Public Health Genomics, University of Virginia
2Department of Public Health Sciences, University of Virginia
3Department of Biomedical Engineering, University of Virginia
4Department of Biochemistry and Molecular Genetics, University of Virginia
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  • For correspondence: nsheffield@virginia.edu
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Abstract

Functional genomics experiments, like ChIP-Seq or ATAC-Seq, produce results that are summarized as a region set. Many tools have been developed to analyze region sets, including computing similarity metrics to compare them. However, there is no way to objectively evaluate the effectiveness of region set similarity metrics. In this paper we present Bedshift, a command-line tool and Python API to generate new BED files by making random perturbations to an original BED file. Perturbed files have known similarity to the original file and are therefore useful to benchmark similarity metrics. To demonstrate, we used Bedshift to create an evaluation dataset of hundreds of perturbed files generated by shifting, adding, and dropping regions from a reference BED file. Then, we compared four similarity metrics: Jaccard score, coverage score, Euclidean distance, and cosine similarity. Our results highlight differences in behavior among these metrics, such as that Jaccard score is most sensitive to added or dropped regions, while coverage score is most sensitive to shifted regions. Together, we show that Bedshift is a useful tool for creating randomized region sets for a variety of uses.

Availability BSD2-licensed source code and documentation can be found at https://bedshift.databio.org.

Competing Interest Statement

The authors have declared no competing interest.

Footnotes

  • A new version of the software, with new configuration options and more powerful features, as well as a completely revised analyses that extended the tests to multiple different computational experiments.

  • https://github.com/databio/bedshift

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 4.0 International license.
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Posted May 10, 2021.
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Bedshift: perturbation of genomic interval sets
Aaron Gu, Hyun Jae Cho, Nathan C. Sheffield
bioRxiv 2020.11.11.378554; doi: https://doi.org/10.1101/2020.11.11.378554
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Bedshift: perturbation of genomic interval sets
Aaron Gu, Hyun Jae Cho, Nathan C. Sheffield
bioRxiv 2020.11.11.378554; doi: https://doi.org/10.1101/2020.11.11.378554

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