High-throughput RNA sequencing (RNA-seq) technology provides a revolutionary approach to studying splicing events de nova. However, identifying splice junctions with high sensitivity and specificity remains a challenge. In the present study, we proposed a new tool named SeqSaw to detect splice junctions with or without the canonical GT-AG splicing signal. SeqSaw was applied to two ENCODE RNA-seq datasets and also compared with two existing methods. It was shown that the proposed method obtained better results on finding novel splice junctions. Experiments also revealed that the current sequencing depth has not yet reached saturation to detect novel transcripts. Moreover, by comparing the number of supporting reads, we demonstrated that many un-annotated splicing events can be tissue specific. (C) 2011 Elsevier Inc. All rights reserved.