Intron-Centric Estimation of Alternative Splicing from RNA-seq data

TitleIntron-Centric Estimation of Alternative Splicing from RNA-seq data
Publication TypeJournal Article
Year of Publication2012
AuthorsPervouchine DD, Knowles DG, Guigó R
Start Page273
Date PublishedNov

MOTIVATION: Novel technologies brought in unprecedented amounts of high-throughput sequencing data along with great challenges in their analysis and interpretation. The percent-spliced-in (PSI, Ψ) metric estimates the incidence of single-exon skipping events and can be computed directly by counting reads that align to known or predicted splice junctions. However, the vast majority of human splicing events are more complex than single-exon skipping. RESULTS: In this short report we present a framework that generalizes the Ψ metric to arbitrary classes of splicing events. We change the view from exon-centric to intron-centric and split the value of Ψ into two indices, ψ(5) and ψ(3), measuring the rate of splicing at the 5'- and 3'-end of the intron, respectively. The advantage of having two separate indices is that they deconvolute two distinct elementary acts of the splicing reaction. The completeness of splicing index (COSI) is decomposed in a similar way. This framework is implemented as bam2ssj, a BAM-file processing pipeline for strand-specific counting of reads that align to splice junctions or overlap with splice sites. It can be used as a consistent protocol for quantifying splice junctions from RNA-seq data since no such standard procedure currently exists. AVAILABILITY: The C(++) code of bam2ssj is open-source and is available at CONTACT: