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Table 1
Software methods and tools for differential expression analysis of RNA-seq
Analysis step	Method	Implementation	References

Mapping	General aligner	GMAP/GSNAP	[91]
		BFAST	[20]
		BOWTIE	[25]
		CloudBurst	[92]
		GNUmap	[93]
		MAQ/BWA	[23]
		PerM	[19]
		RazerS	[94]
		Mrfast/mrsfast	[22]
		SOAP/SOAP2	[24,95]
		SHRiMP	[21]
	De novo annotator	QPALMA/GenomeMapper/PALMapper	[37]
		SpliceMap	[96]
		SOAPals	[95]
		G-Mo.R-Se	[97]
		TopHat	[40]
		SplitSeek	[36]
	De novo transcript assembler	Oases	[98]
		MIRA	[99]
Summarization	Isoform-based	Cufflinks	[11]
		ALEXA-seq	[10]
	Gene-based	Count exons only	For example, [34,45]
		Exon junction libraries	[34,44]
Normalization	Library size		For example, [34]
	RPKM	ERANGE	[32]
	TMM	edgeR	[48]
	Upper quartile	Myrna	[45,47]
Differential expression	Poisson GLM	DEGseq	[100]
		Myrna	[47]
	Negative binomial	edgeR	[57]
		DESeq	[46]
		baySeq	[58]
Systems biology	Gene Ontology analysis	GOseq	[68]

Abbreviations: GLM, generalized linear model; RPKM, reads per kilobase of exon model per million mapped reads; TMM, trimmed mean of M-values.
Oshlack et al. Genome Biology 2010 11:220 doi:10.1186/gb-2010-11-12-220

Table 1