abstract

ROP: Dumpster Diving in RNA-sequencing to Find the Source of 1 Trillion Reads Across Diverse Adult Human Tissues

Authors:

Serghei Mangul,

Noah ZaitlenAuthors Info & Claims

BCB '18: Proceedings of the 2018 ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics

Page 573

https://doi.org/10.1145/3233547.3233726

Published: 15 August 2018 Publication History

Abstract

High-throughput RNA-sequencing (RNA-seq) technologies provide an unprecedented opportunity to explore the individual transcriptome. Unmapped reads are a large and often overlooked output of standard RNA-seq analyses. Here, we present Read Origin Protocol (ROP), a tool for discovering the source of all reads originating from complex RNA molecules. We apply ROP to samples across 2630 individuals from 54 diverse human tissues. Our approach can account for 99.9% of 1 trillion reads of various read length. Additionally, we use ROP to investigate the functional mechanisms underlying connections between the immune system, microbiome, and disease. ROP is freely available at https://github.com/smangul1/rop/wiki.

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Cited By

Mangul SYang HStrauli NGruhl FPorath HHsieh KChen LDaley TChristenson SWesolowska-Andersen ASpreafico RRios CEng CSmith AHernandez ROphoff RSantana JLevanon EWoodruff PBurchard ESeibold MShifman SEskin EZaitlen N(2018)ROP: dumpster diving in RNA-sequencing to find the source of 1 trillion reads across diverse adult human tissuesGenome Biology10.1186/s13059-018-1403-719:1Online publication date: 15-Feb-2018
https://doi.org/10.1186/s13059-018-1403-7

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cover image ACM Conferences

BCB '18: Proceedings of the 2018 ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics

August 2018

727 pages

ISBN:9781450357944

DOI:10.1145/3233547

General Chairs:
Amarda Shehu
George Mason University, USA
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Cathy Wu
University of Delaware, USA
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Program Chairs:
Christina Boucher
University of Florida, USA
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Jing Li
Case Western Reserve University, USA
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Hongfang Liu
Mayo Clinic, USA
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Mihai Pop
University of Maryland, USA

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Published: 15 August 2018

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Cited By

Mangul SYang HStrauli NGruhl FPorath HHsieh KChen LDaley TChristenson SWesolowska-Andersen ASpreafico RRios CEng CSmith AHernandez ROphoff RSantana JLevanon EWoodruff PBurchard ESeibold MShifman SEskin EZaitlen N(2018)ROP: dumpster diving in RNA-sequencing to find the source of 1 trillion reads across diverse adult human tissuesGenome Biology10.1186/s13059-018-1403-719:1Online publication date: 15-Feb-2018
https://doi.org/10.1186/s13059-018-1403-7

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