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RNA-Seq is being increasingly adopted as the technology of choice for gene expression studies, and with large numbers of experiments producing partial transcripts of genes, it is expected that there will be rapid progress in the coming years in annotating genomes. As more complete genome annotations are produced, it is increasingly desirable to include them in analyses rather than assembling transcripts ‘from scratch’ with every new experiment. The reference annotation-based transcript assembly approach we have introduced addresses this problem, and allows for the incremental improvement of annotations with RNA-Seq experiments. It is also convenient in that novel genes and transcripts (with respect to an existing annotation) are easily extracted from the output of our assembler.
(Roberts et al., 2011) Identification of novel transcripts in annotated genomes using RNA-Seq. Bioinformatics.