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DiffSplice: the genome-wide detection of differential splicing events with RNA-seq

https://doi.org/10.1093/nar/gks1026

Hu, Yin; Huang, Yan; Du, Ying; Orellana, Christian F.; Singh, Darshan; Johnson, Amy R.; Monroy, Anaïs; Kuan, Pei-Fen; Hammond, Scott M.; Makowski, Liza; et al (November 2012, Nucleic Acids Research)

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MapSplice: Accurate mapping of RNA-seq reads for splice junction discovery

https://doi.org/10.1093/nar/gkq622

Wang, Kai; Singh, Darshan; Zeng, Zheng; Coleman, Stephen J.; Huang, Yan; Savich, Gleb L.; He, Xiaping; Mieczkowski, Piotr; Grimm, Sara A.; Perou, Charles M.; et al (August 2010, Nucleic Acids Research)

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A probabilistic framework for aligning paired-end RNA-seq data

https://doi.org/10.1093/bioinformatics/btq336

Hu, Yin; Wang, Kai; He, Xiaping; Chiang, Derek Y.; Prins, Jan F.; Liu, Jinze (June 2010, Bioinformatics)

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