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pyBedGraph: a Python package for fast operations on 1-dimensional genomic signal tracks

Henry B. Zhang, Minji Kim, Jeffrey H. Chuang, Yijun Ruan
doi: https://doi.org/10.1101/709683
Henry B. Zhang
1Department of Electrical and Computer Engineering, University of California, San Diego, La Jolla, CA, USA
2The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
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Minji Kim
2The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
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  • For correspondence: minji.kim@jax.org
Jeffrey H. Chuang
2The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
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Yijun Ruan
2The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
3Department of Genetics and Genome Sciences, University of Connecticut Health Center, Farmington, CT, USA
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Abstract

Motivation Modern genomic research relies heavily on next-generation sequencing experiments such as ChIP-seq and ChIA-PET that generate coverage files for transcription factor binding, as well as DHS and ATAC-seq that yield coverage files for chromatin accessibility. Such files are in a bedGraph text format or a bigWig binary format. Obtaining summary statistics in a given region is a fundamental task in analyzing protein binding intensity or chromatin accessibility. However, the existing Python package for operating on coverage files is not optimized for speed.

Results We developed pyBedGraph, a Python package to quickly obtain summary statistics for a given interval in a bedGraph file. When tested on 8 ChIP-seq and ATAC-seq datasets, pyBedGraph is on average 245 times faster than the existing program. Notably, pyBedGraph can look up the exact mean signal of 1 million regions in ~0.26 second on a conventional laptop. An approximate mean for 10,000 regions can be computed in ~0.0012 second with an error rate of less than 5 percent.

Availability pyBedGraph is publicly available at https://github.com/TheJacksonLaboratory/pyBedGraph under the MIT license.

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-ND 4.0 International license.
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Posted July 20, 2019.
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pyBedGraph: a Python package for fast operations on 1-dimensional genomic signal tracks
Henry B. Zhang, Minji Kim, Jeffrey H. Chuang, Yijun Ruan
bioRxiv 709683; doi: https://doi.org/10.1101/709683
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pyBedGraph: a Python package for fast operations on 1-dimensional genomic signal tracks
Henry B. Zhang, Minji Kim, Jeffrey H. Chuang, Yijun Ruan
bioRxiv 709683; doi: https://doi.org/10.1101/709683

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