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LeafCutter vs. MAJIQ and comparing software in the fast moving field of genomics

Jorge Vaquero-Garcia, Scott Norton, Yoseph Barash
doi: https://doi.org/10.1101/463927
Jorge Vaquero-Garcia
1Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
2Department of Computer and Information Science, School of Engineering, University of Pennsylvania, Philadelphia, PA, 19104, USA
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Scott Norton
2Department of Computer and Information Science, School of Engineering, University of Pennsylvania, Philadelphia, PA, 19104, USA
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Yoseph Barash
1Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
2Department of Computer and Information Science, School of Engineering, University of Pennsylvania, Philadelphia, PA, 19104, USA
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  • For correspondence: yosephb@upenn.edu
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Abstract

In a recent publication, Li et al. introduced LeafCutter, a new method for detecting and quantifying differential splicing of RNA from RNASeq data. In this work, Li et al. first compared LeafCutter to existing methods, then used it for a study of splicing variations and sQTL analysis from a large set of GTEx samples. While the study was elaborate and comprehensive, we want to highlight several issues with the comparative analysis performed by Li et al. We argue these issues created an inaccurate and misleading representation of other tools, namely MAJIQ and rMATS. More broadly, we believe the points we raise regarding the comparative analysis by Li et al. are representative of general issues we all, as authors, editors, and reviewers, are faced with and must address in the current times of fast paced genomics and computational research.

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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 4.0 International license.
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Posted November 08, 2018.
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LeafCutter vs. MAJIQ and comparing software in the fast moving field of genomics
Jorge Vaquero-Garcia, Scott Norton, Yoseph Barash
bioRxiv 463927; doi: https://doi.org/10.1101/463927
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LeafCutter vs. MAJIQ and comparing software in the fast moving field of genomics
Jorge Vaquero-Garcia, Scott Norton, Yoseph Barash
bioRxiv 463927; doi: https://doi.org/10.1101/463927

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