A benchmark for RNA-seq quantification pipelines

Table 2 Summarized metrics for analyzed pipelines based on a simulation dataset

Method	SD low	SD medium	SD high	NE (K = 1)	NN (K = 1)	TxDiff low	TxDiff medium	TxDiff high	deFC low	deFC medium	deFC high	pAUC
Cufflinks	0.73 (0.002)	0.54 (0.003)	0.26 (0.001)	0.090	0.657	0.34 (0.011)	0.08 (0.003)	0.05 (0.003)	0.53 (0.009)	0.95 (0.006)	0.98 (0.003)	0.61
eXpress	0.71 (0.003)	0.67 (0.004)	0.30 (0.001)	0.09	0.68	0.33 (0.009)	0.07 (0.003)	0.07 (0.003)	0.47 (0.011)	0.87 (0.015)	0.91 (0.012)	0.60
Flux Capacitor	1.03 (0.004)	1.23 (0.007)	0.40 (0.002)	0.15	0.63	0.46 (0.013)	0.15 (0.006)	0.07 (0.004)	0.39 (0.011)	0.82 (0.013)	0.97 (0.009)	0.52
Kallisto	0.72 (0.003)	0.55 (0.003)	0.27 (0.001)	0.10	0.63	0.37 (0.011)	0.08 (0.004)	0.05 (0.003)	0.56 (0.008)	0.95 (0.006)	0.98 (0.002)	0.58
RSEM	0.65 (0.002)	0.48 (0.003)	0.25 (0.001)	0.08	0.69	0.43 (0.011)	0.07 (0.004)	0.04 (0.003)	0.58 (0.008)	0.96 (0.006)	1.00 (0.003)	0.65
Sailfish	0.76 (0.003)	0.65 (0.004)	0.30 (0.001)	0.11	0.57	0.34 (0.009)	0.08 (0.004)	0.05 (0.003)	0.52 (0.011)	0.94 (0.011)	0.96 (0.006)	0.56
Salmon	0.64 (0.002)	0.52 (0.003)	0.26 (0.001)	0.09	0.67	0.35 (0.010)	0.08 (0.004)	0.05 (0.003)	0.54 (0.008)	0.95 (0.007)	1.00 (0.003)	0.61

The last four columns are based on differential expression of transcripts. pAUC partial area under the receiver operating characteristic curve