TY - JOUR
T1 - ROP
T2 - Dumpster diving in RNA-sequencing to find the source of 1 trillion reads across diverse adult human tissues
AU - Mangul, Serghei
AU - Yang, Harry Taegyun
AU - Strauli, Nicolas
AU - Gruhl, Franziska
AU - Porath, Hagit T.
AU - Hsieh, Kevin
AU - Chen, Linus
AU - Daley, Timothy
AU - Christenson, Stephanie
AU - Wesolowska-Andersen, Agata
AU - Spreafico, Roberto
AU - Rios, Cydney
AU - Eng, Celeste
AU - Smith, Andrew D.
AU - Hernandez, Ryan D.
AU - Ophoff, Roel A.
AU - Santana, Jose Rodriguez
AU - Levanon, Erez Y.
AU - Woodruff, Prescott G.
AU - Burchard, Esteban
AU - Seibold, Max A.
AU - Shifman, Sagiv
AU - Eskin, Eleazar
AU - Zaitlen, Noah
N1 - Publisher Copyright:
© 2018 The Author(s).
PY - 2018/2/15
Y1 - 2018/2/15
N2 - 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.
AB - 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.
UR - http://www.scopus.com/inward/record.url?scp=85043995439&partnerID=8YFLogxK
U2 - 10.1186/s13059-018-1403-7
DO - 10.1186/s13059-018-1403-7
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C2 - 29548336
AN - SCOPUS:85043995439
SN - 1474-7596
VL - 19
JO - Genome Biology
JF - Genome Biology
IS - 1
M1 - 36
ER -