FineSplice – enhanced splice junction detection and quantification

Alternative splicing is the main mechanism governing protein diversity. The recent developments in RNA-Seq technology have enabled the study of the global impact and regulation of this biological process. However, the lack of standardized protocols constitutes a major bottleneck in the analysis of alternative splicing. This is particularly important for the identification of exon-exon junctions, which is a critical step in any analysis workflow.

Here researchers at the National Center for Cardiovascular Research, Spain performed a systematic benchmarking of alignment tools to dissect the impact of design and method on the mapping, detection and quantification of splice junctions from multi-exon reads. Accordingly, they devised a novel pipeline based on TopHat2 combined with a splice junction detection algorithm, which they have named FineSplice. FineSplice allows effective elimination of spurious junction hits arising from artefactual alignments, achieving up to 99% precision in both real and simulated data sets and yielding superior F1 scores under most tested conditions. The proposed strategy conjugates an efficient mapping solution with a semi-supervised anomaly detection scheme to filter out false positives and allows reliable estimation of expressed junctions from the alignment output. Ultimately this provides more accurate information to identify meaningful splicing patterns.


Availability – FineSplice is freely available at

Gatto A1, Torroja-Fungairiño C, Mazzarotto F, Cook SA, Barton PJ, Sánchez-Cabo F, Lara-Pezzi E. (2014) FineSplice, enhanced splice junction detection and quantification: a novel pipeline based on the assessment of diverse RNA-Seq alignment solutions. Nucleic Acids Res [Epub ahead of print]. [article]