PASSion: a pattern growth algorithm-based pipeline for splice junction detection in paired-end RNA-Seq data.

ABSTRACT:

Motivation

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 perf

SUBMITTER: Zhang Y 

PROVIDER: S-EPMC3278765 | biostudies-literature | 2012 Feb

REPOSITORIES: biostudies-literature