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Dumpster diving in RNA-sequencing to find the source of every last read

Serghei Mangul, Harry Taegyun Yang, Nicolas Strauli, Franziska Gruhl, Timothy Daley, Stephanie Christenson, Agata Wesolowska-Andersen, Roberto Spreafico, Cydney Rios, Celeste Eng, Andrew D. Smith, Ryan D. Hernandez, Roel A. Ophoff, Jose Rodriguez Santana, Prescott G. Woodruff, Esteban Burchard, Max A. Seibold, Sagiv Shifman, Eleazar Eskin, Noah Zaitlen
doi: https://doi.org/10.1101/053041
Serghei Mangul
1Department of Computer Science, University of California Los Angeles, Los Angeles, USA
2Institute for Quantitative and Computational Biosciences, University of California Los Angeles, Los Angeles, USA
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  • For correspondence: smangul@ucla.edu Noah.Zaitlen@ucsf.edu
Harry Taegyun Yang
1Department of Computer Science, University of California Los Angeles, Los Angeles, USA
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Nicolas Strauli
3Biomedical Sciences Graduate Program, University of California, San Francisco, CA, USA
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Franziska Gruhl
4Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
5Swiss Institute of Bioinformatics, Lausanne, Switzerland
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Timothy Daley
6Department of Molecular and Computational Biology, University of Southern California, CA, USA
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Stephanie Christenson
7Division of Pulmonary, Critical Care, Sleep and Allergy, Department of Medicine, and Cardiovascular Research Institute, University of California, San Francisco, CA, USA
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Agata Wesolowska-Andersen
8Center for Genes, Environment, and Health, National Jewish Health, Denver, CO, USA
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Roberto Spreafico
2Institute for Quantitative and Computational Biosciences, University of California Los Angeles, Los Angeles, USA
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Cydney Rios
8Center for Genes, Environment, and Health, National Jewish Health, Denver, CO, USA
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Celeste Eng
9Department of Medicine, University of California, San Francisco, CA, USA
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Andrew D. Smith
6Department of Molecular and Computational Biology, University of Southern California, CA, USA
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Ryan D. Hernandez
10Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA, USA
11Institute for Quantitative Biosciences, University of California, San Francisco, CA, USA
12Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
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Roel A. Ophoff
13Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, University California Los Angeles, Los Angeles, USA
14Department of Human Genetics, University of California Los Angeles, Los Angeles, USA
15Department of Psychiatry, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht, The Netherlands
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Jose Rodriguez Santana
16Pediatric Pulmonology, San Juan, Puerto Rico
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Prescott G. Woodruff
7Division of Pulmonary, Critical Care, Sleep and Allergy, Department of Medicine, and Cardiovascular Research Institute, University of California, San Francisco, CA, USA
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Esteban Burchard
9Department of Medicine, University of California, San Francisco, CA, USA
10Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA, USA
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Max A. Seibold
8Center for Genes, Environment, and Health, National Jewish Health, Denver, CO, USA
17Department of Pediatrics, National Jewish Health, Denver, CO, USA
18University of Colorado School of Medicine, Denver CO, USA
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Sagiv Shifman
19Department of Genetics, The Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
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Eleazar Eskin
1Department of Computer Science, University of California Los Angeles, Los Angeles, USA
14Department of Human Genetics, University of California Los Angeles, Los Angeles, USA
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Noah Zaitlen
9Department of Medicine, University of California, San Francisco, CA, USA
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  • For correspondence: smangul@ucla.edu Noah.Zaitlen@ucsf.edu
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Article Information

doi 
https://doi.org/10.1101/053041
History 
  • May 13, 2016.

Article Versions

  • You are currently viewing Version 1 of this article (May 13, 2016 - 02:40).
  • View Version 2, the most recent version of this article.
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.

Author Information

  1. Serghei Mangul#,1,2,
  2. Harry Taegyun Yang1,
  3. Nicolas Strauli3,
  4. Franziska Gruhl4,5,
  5. Timothy Daley6,
  6. Stephanie Christenson7,
  7. Agata Wesolowska-Andersen8,
  8. Roberto Spreafico2,
  9. Cydney Rios8,
  10. Celeste Eng9,
  11. Andrew D. Smith6,
  12. Ryan D. Hernandez10,11,12,
  13. Roel A. Ophoff13,14,15,
  14. Jose Rodriguez Santana16,
  15. Prescott G. Woodruff7,
  16. Esteban Burchard9,10,
  17. Max A. Seibold*8,17,18,
  18. Sagiv Shifman*19,
  19. Eleazar Eskin*1,14 and
  20. Noah Zaitlen*#,9
  1. 1Department of Computer Science, University of California Los Angeles, Los Angeles, USA
  2. 2Institute for Quantitative and Computational Biosciences, University of California Los Angeles, Los Angeles, USA
  3. 3Biomedical Sciences Graduate Program, University of California, San Francisco, CA, USA
  4. 4Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
  5. 5Swiss Institute of Bioinformatics, Lausanne, Switzerland
  6. 6Department of Molecular and Computational Biology, University of Southern California, CA, USA
  7. 7Division of Pulmonary, Critical Care, Sleep and Allergy, Department of Medicine, and Cardiovascular Research Institute, University of California, San Francisco, CA, USA
  8. 8Center for Genes, Environment, and Health, National Jewish Health, Denver, CO, USA
  9. 9Department of Medicine, University of California, San Francisco, CA, USA
  10. 10Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA, USA
  11. 11Institute for Quantitative Biosciences, University of California, San Francisco, CA, USA
  12. 12Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
  13. 13Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, University California Los Angeles, Los Angeles, USA
  14. 14Department of Human Genetics, University of California Los Angeles, Los Angeles, USA
  15. 15Department of Psychiatry, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht, The Netherlands
  16. 16Pediatric Pulmonology, San Juan, Puerto Rico
  17. 17Department of Pediatrics, National Jewish Health, Denver, CO, USA
  18. 18University of Colorado School of Medicine, Denver CO, USA
  19. 19Department of Genetics, The Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
  1. ↵#Correspondence to: Serghei Mangul smangul{at}ucla.edu and Noah Zaitlen Noah.Zaitlen{at}ucsf.edu
  1. ↵* Equal contribution

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Dumpster diving in RNA-sequencing to find the source of every last read
Serghei Mangul, Harry Taegyun Yang, Nicolas Strauli, Franziska Gruhl, Timothy Daley, Stephanie Christenson, Agata Wesolowska-Andersen, Roberto Spreafico, Cydney Rios, Celeste Eng, Andrew D. Smith, Ryan D. Hernandez, Roel A. Ophoff, Jose Rodriguez Santana, Prescott G. Woodruff, Esteban Burchard, Max A. Seibold, Sagiv Shifman, Eleazar Eskin, Noah Zaitlen
bioRxiv 053041; doi: https://doi.org/10.1101/053041
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Dumpster diving in RNA-sequencing to find the source of every last read
Serghei Mangul, Harry Taegyun Yang, Nicolas Strauli, Franziska Gruhl, Timothy Daley, Stephanie Christenson, Agata Wesolowska-Andersen, Roberto Spreafico, Cydney Rios, Celeste Eng, Andrew D. Smith, Ryan D. Hernandez, Roel A. Ophoff, Jose Rodriguez Santana, Prescott G. Woodruff, Esteban Burchard, Max A. Seibold, Sagiv Shifman, Eleazar Eskin, Noah Zaitlen
bioRxiv 053041; doi: https://doi.org/10.1101/053041

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