Table S2. Performance of four transcript assembly programs in capturing exon skipping events from simulated RNA-seq data. Recall = TP/(TP+FN), Precision = TP/(TP+FP).

Exon skipping (ES)
	Predicted	Correct	Recall	Precision
Cufflinks	632	561	0.42	0.89
IsoCEM	940	496	0.37	0.53
SLIDE	3022	311	0.23	0.10
Scripture	1724	1045	0.78	0.61