SpliceMap – a de novo splice junction discovery tool

Alternative splicing is a prevalent post-transcriptional process, which is not only important to normal cellular function but is also involved in human diseases. The newly developed second generation sequencing technique provides high-throughput data (RNA-seq data) to study alternative splicing events in different types of cells.

Here, the authors present a computational method, SpliceMap, to detect splice junctions from RNA-seq data. This method does not depend on any existing annotation of gene structures and is capable of finding novel splice junctions with high sensitivity and specificity. It can handle long reads (50-100 nt) and can exploit paired-read information to improve mapping accuracy. Several parameters are included in the output to indicate the reliability of the predicted junction and help filter out false predictions.

They applied SpliceMap to analyze 23 million paired 50-nt reads from human brain tissue. The results show at this depth of sequencing, RNA-seq can support reliable detection of splice junctions except for those that are present at very low level. Compared to current methods, SpliceMap can achieve 12% higher sensitivity without sacrificing specificity.

SpliceMap is open access and the code is available here.

Kin Fai Au, Hui Jiang, Lan Lin, Yi Xing, and Wing Hung Wong (2010) Detection of splice junctions from paired-end RNA-seq data by SpliceMap Nucleic Acids Research [Epub ahead of print]. [article]