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MOCCASIN: A method for correcting for known and unknown confounders in RNA splicing analysis

Barry Slaff, View ORCID ProfileCaleb M Radens, Paul Jewell, Anupama Jha, Nicholas F Lahens, Gregory R Grant, View ORCID ProfileAndrei Thomas-Tikhonenko, Kristen W. Lynch, View ORCID ProfileYoseph Barash
doi: https://doi.org/10.1101/2020.06.16.154674
Barry Slaff
1Department of Computer and Information Sciences, School of Engineering, University of Pennsylvania, Philadelphia PA 19104
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Caleb M Radens
2Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia PA 19104
4Graduate Group in Cell and Molecular Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia PA 19104
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  • ORCID record for Caleb M Radens
Paul Jewell
2Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia PA 19104
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Anupama Jha
1Department of Computer and Information Sciences, School of Engineering, University of Pennsylvania, Philadelphia PA 19104
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Nicholas F Lahens
3Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia PA 19104
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Gregory R Grant
2Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia PA 19104
3Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia PA 19104
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Andrei Thomas-Tikhonenko
6Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia PA 19104
7Division of Cancer Pathobiology, Children’s Hospital of Philadelphia, Philadelphia PA 19104
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Kristen W. Lynch
2Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia PA 19104
4Graduate Group in Cell and Molecular Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia PA 19104
5Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia PA 19104
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Yoseph Barash
1Department of Computer and Information Sciences, School of Engineering, University of Pennsylvania, Philadelphia PA 19104
2Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia PA 19104
4Graduate Group in Cell and Molecular Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia PA 19104
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  • ORCID record for Yoseph Barash
  • For correspondence: yosephb@upenn.edu
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Abstract

While the effects of confounders on gene expression analysis have been extensively studied there is a lack of equivalent analysis and tools for RNA splicing analysis. Here we assess the effect of confounders in two large public RNA-Seq datasets (TARGET, ENCODE), develop a new method, MOCCASIN, to correct the effect of both known and unknown confounders on RNA splicing quantification, and demonstrate MOCCASIN’s effectiveness on both synthetic and real data.

Competing Interest Statement

The authors have declared no competing interest.

Footnotes

  • http://majiq.biociphers.org/

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 June 17, 2020.
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MOCCASIN: A method for correcting for known and unknown confounders in RNA splicing analysis
Barry Slaff, Caleb M Radens, Paul Jewell, Anupama Jha, Nicholas F Lahens, Gregory R Grant, Andrei Thomas-Tikhonenko, Kristen W. Lynch, Yoseph Barash
bioRxiv 2020.06.16.154674; doi: https://doi.org/10.1101/2020.06.16.154674
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MOCCASIN: A method for correcting for known and unknown confounders in RNA splicing analysis
Barry Slaff, Caleb M Radens, Paul Jewell, Anupama Jha, Nicholas F Lahens, Gregory R Grant, Andrei Thomas-Tikhonenko, Kristen W. Lynch, Yoseph Barash
bioRxiv 2020.06.16.154674; doi: https://doi.org/10.1101/2020.06.16.154674

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