Table 4.

Detected AS types or differentially spliced isoforms of these tools. If the tools can detect the splice junctions, the precise AS events are listed in the right column.

Tools	Can Quantify Differential Expression of Isoforms		Can Detect Splice Junctions	SE	MXE	RI	A5SS	A3SS	AFE	ALE	NSS&RS	CS	DNSJ
	Within One Condition	Between Two Conditions
Alt Event Finder	no	no	yes	yes	no	no	no	no	no	no	no	no	yes
SpliceMap	no	no	yes	yes	yes	yes	yes	yes	yes	yes	no	no	yes
FineSplice	no	no	yes	yes	yes	yes	yes	yes	yes	yes	no	no	yes
RSW	no	no	yes	yes	yes	yes	yes	yes	yes	yes	no	yes	yes
RSR	no	no	yes	yes	yes	yes	yes	yes	yes	yes	no	yes	yes
PASTA	no	no	yes	yes	yes	yes	yes	yes	yes	yes	no	no	yes
rMATS	no	yes	yes	yes	yes	yes	yes	yes	no	no	no	no	no
SOAPsplice	no	no	yes	yes	yes	yes	yes	yes	yes	yes	no	no	yes
SplicePie	no	no	yes	yes	no	yes	no	no	no	no	yes	no	yes
SplicingCompass	no	yes	no	no	no	no	no	no	no	no	no	no	no
TopHat	no	no	yes	yes	yes	yes	yes	yes	yes	yes	no	no	yes
TrueSight	no	no	yes	yes	yes	yes	yes	yes	yes	yes	no	no	yes
NSMAP	yes	no	yes	yes	yes	yes	yes	yes	yes	yes	no	no	yes
rSeqDiff	no	yes	no	no	no	no	no	no	no	no	no	no	no
rSeqNP	no	yes	no	no	no	no	no	no	no	no	no	no	no

The abbreviations are as follows: cassette exon (also called exon skipping or skipped exon): SE; mutually exclusive exons: MXE; retention of intron: RI; alternative 5’ splicing site (5’ss): A5SS; alternative 3’ splicing site (3’ss): A3SS; alternative first exon: AFE; alternative last exon: ALE; non-sequential splicing and recursive splicing: NSS&RS; cytosol splicing: CS; de novel splice junction: DNSJ.