PASSion: a pattern growth algorithm-based pipeline for splice junction detection in paired-end RNA-Seq data.
BACKGROUND
RNA-seq is a powerful technology for the study of transcriptome profiles that uses deep-sequencing technologies. Moreover, it may be used for cellular phenotyping and help establishing the etiology of diseases characterized by abnormal splicing patterns. In RNA-Seq, the exact nature of splicing events is buried in the reads that span exon-exon boundaries. The accurate and efficient mapping of these reads to the reference genome is a major challenge.


RESULTS
We developed PASSion, a pattern growth algorithm-based pipeline for splice site detection in paired-end RNA-Seq reads. Comparing the performance of PASSion to three existing RNA-Seq analysis pipelines, TopHat, MapSplice and HMMSplicer, revealed that PASSion is competitive with these packages. Moreover, the performance of PASSion is not affected by read length and coverage. It performs better than the other three approaches when detecting junctions in highly abundant transcripts. PASSion has the ability to detect junctions that do not have known splicing motifs, which cannot be found by the other tools. Of the two public RNA-Seq datasets, PASSion predicted ≈ 137,000 and 173,000 splicing events, of which on average 82 are known junctions annotated in the Ensembl transcript database and 18% are novel. In addition, our package can discover differential and shared splicing patterns among multiple samples.


BACKGROUND
The code and utilities can be freely downloaded from https://trac.nbic.nl/passion and ftp://ftp.sanger.ac.uk/pub/zn1/passion.
Department of Molecular Epidemiology, Medical Statistics and Bioinformatics, Leiden University Medical Center, Leiden, The Netherlands. y.zhang@lumc.nl
Yanju
Y
Zhang
Eric-Wubbo
EW
Lameijer
Peter A C
PA
't Hoen
Zemin
Z
Ning
P Eline
PE
Slagboom
Kai
K
Ye
D000465:Algorithms; D002886:Chromosomes, Human, Pair 17; D005091:Exons; D020869:Gene Expression Profiling; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D012313:RNA / Q000235:genetics; D022821:RNA Splice Sites; D012326:RNA Splicing; D017423:Sequence Analysis, RNA / Q000379:methods*; D012984:Software
D022821:RNA Splice Sites; D012313:RNA