RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome

BMC Bioinformatics

Table 2 Correlation of quantification method predictions with MAQC qRT-PCR values

SRA ID	Read type	Sample	RSEM	IsoEM	IsoEM (C)	Cufflinks	Cufflinks (C)	rQuant
SRX016366	SE	HBR	0.69	0.68	0.68	0.71	0.79	0.72
SRX003926	SE	HBR	0.68	0.67	0.67	0.7	0.73	0.71
SRX018974	PE	HBR	0.69	0.69	0.69	0.69	0.78	NA
SRX016368	SE	UHR	0.71	0.71	0.72	0.72	0.77	0.72
SRX016369	SE	UHR	0.73	0.74	0.74	0.73	0.76	0.74
SRX016370	SE	UHR	0.74	0.75	0.75	0.74	0.77	0.75
SRX016371	SE	UHR	0.74	0.75	0.75	0.74	0.77	0.75
SRX016372	SE	UHR	0.75	0.75	0.75	0.74	0.77	0.76
SRX003927	SE	UHR	0.72	0.71	0.72	0.71	0.74	0.72

Correlation values (Pearson r² of log-transformed abundance values) were computed between the predictions of four methods and "gold-standard" values from qRT-PCR for nine different RNA-Seq data sets. IsoEM and Cufflinks were run with (C) and without their bias correction modes.

ISSN: 1471-2105