PASSion uses the mapped read in a pair as anchor and then uses a high resolution algorithm, pattern growth, to remap the proximal and distal fragments of the unmapped read to a local region of the reference indicated by the mate. It is capable of identifying both known and novel canonical and non-canonical junctions with SNP or sequencing error tolerance.
Yanju Zhang (Leiden University Medical Center, The Netherlands): y.zhang AT lumc.nl
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PASSion: A Pattern Growth Algorithm Based Pipeline for Splice Junction Detection in Paired-end RNA-Seq Data
Yanju Zhang; Eric-Wubbo Lameijer; Peter A.C. ‘t Hoen; Zemin Ning; P. Eline Slagboom; Kai Ye
Bioinformatics 2012; doi: 10.1093/bioinformatics/btr712