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Transcriptome sequencing (RNA-Seq) overcomes limitations of previously used RNA quantification methods and provides one experimental framework for both high-throughput characterization and quantification of transcripts at the nucleotide level. The first step and a major challenge in the analysis of such experiments is the mapping of sequencing reads to a transcriptomic origin including the identification of splicing events.
(Lindner and Friedel, 2012) A comprehensive evaluation of alignment algorithms in the context of RNA-seq. PLoS One.