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TrueSight: a new algorithm for splice junction detection using RNA-seq

Yang Li, Hongmei Li-Byarlay, Paul Burns, Mark Borodovsky, Gene E. Robinson, Jian Ma
2012 Nucleic Acids Research  
RNA-seq has proven to be a powerful technique for transcriptome profiling based on next-generation sequencing (NGS) technologies.  ...  The model is further utilized in a machine-learning approach to precisely identify SJs.  ...  ACKNOWLEDGEMENTS We thank A. Hernandez and the W. M. Keck Center for Comparative and Functional Genomics at the University of Illinois for library preparation and RNA-seq; T.  ... 
doi:10.1093/nar/gks1311 pmid:23254332 pmcid:PMC3575843 fatcat:cxnte5gknbasvnjvnydkovpgyq

Computational approaches for improving the accuracy and efficiency of RNA-seq analysis [article]

Hirak N/A Sarkar
2020
By employing equivalence classes at cellular resolution, I have developed a droplet-based single-cell RNA-seq sequence simulator capabl [...]  ...  I used the equivalence classes for a number of applications in both single-cell and bulk RNA-seq technologies.  ...  To mention a few in the transcriptomic world the sequencing technology ranges from RNA transcription (PRO-Seq, GRO-Seq) to RNA-protein interactions (RIP-Seq, Pol II CLIP), RNA Structure (SHAPE-Seq) to  ... 
doi:10.13016/tuy4-kjcc fatcat:zdyqefenpbb4rhwejvuwbtbgjy