A benchmark for RNA-seq quantification pipelines.
Obtaining RNA-seq measurements involves a complex data analytical process with a large number of competing algorithms as options. There is much debate about which of these methods provides the best approach. Unfortunately, it is currently difficult to evaluate their performance due in part to a lack of sensitive assessment metrics. We present a series of statistical summaries and plots to evaluate the performance in terms of specificity and sensitivity, available as a R/Bioconductor package ( http://bioconductor.org/packages/rnaseqcomp ). Using two independent datasets, we assessed seven competing pipelines. Performance was generally poor, with two methods clearly underperforming and RSEM slightly outperforming the rest.
Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA, 02215, USA.|Department of Biostatistics, Harvard TH Chan School of Public Health, 677 Huntington Avenue, Boston, MA, 02115, USA.|School of Computer Science and Technology, Harbin Institute of Technology, Harbin, China.
Mingxiang
M
Teng
Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA, 02215, USA.|Department of Biostatistics, Harvard TH Chan School of Public Health, 677 Huntington Avenue, Boston, MA, 02115, USA.
Michael I
MI
Love
Functional Genomics Group, Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY, 11724, USA.
Carrie A
CA
Davis
Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG) and UPF, Doctor Aiguader, 88, Barcelona, 08003, Spain.
Sarah
S
Djebali
Functional Genomics Group, Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY, 11724, USA.
Alexander
A
Dobin
Department of Genetics and Genome Sciences, Institute for System Genomics, UConn Health Center, Farmington, CT, 06030, USA.
Brenton R
BR
Graveley
Department of Physiology and Biophysics, Weill Cornell Medical College, New York, New York, USA.
Sheng
S
Li
Department of Physiology and Biophysics, Weill Cornell Medical College, New York, New York, USA.
Christopher E
CE
Mason
Department of Genetics and Genome Sciences, Institute for System Genomics, UConn Health Center, Farmington, CT, 06030, USA.
Sara
S
Olson
Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG) and UPF, Doctor Aiguader, 88, Barcelona, 08003, Spain.
Dmitri
D
Pervouchine
Department of Genetics, Stanford University, 300 Pasteur Drive, MC-5477, Stanford, CA, 94305, USA.
Cricket A
CA
Sloan
Department of Genetics and Genome Sciences, Institute for System Genomics, UConn Health Center, Farmington, CT, 06030, USA.
Xintao
X
Wei
Department of Genetics and Genome Sciences, Institute for System Genomics, UConn Health Center, Farmington, CT, 06030, USA.
Lijun
L
Zhan
Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA, 02215, USA. rafa@jimmy.harvard.edu.|Department of Biostatistics, Harvard TH Chan School of Public Health, 677 Huntington Avenue, Boston, MA, 02115, USA. rafa@jimmy.harvard.edu.
Rafael A
RA
Irizarry
D000465:Algorithms; D000818:Animals; D006801:Humans; D012016:Reference Values; D012680:Sensitivity and Specificity; D017423:Sequence Analysis, RNA / Q000379:methods* / Q000592:standards