8.4 Other applications of RNA-seq

RNA-seq generates valuable data that contains information not only at the gene level but also at the level of exons and transcripts. Moreover, the kind of information that we can extract from RNA-seq is not limited to expression quantification. It is possible to detect alternative splicing events such as novel isoforms (Trapnell, Williams, Pertea, et al. 2010), and differential usage of exons (Anders, Reyes, and Huber 2012). It is also possible to observe sequence variants (substitutions, insertions, deletions, RNA-editing) that may change the translated protein product (McKenna, Hanna, Banks, et al. 2010). In the context of cancer genomes, gene-fusion events can be detected with RNA-seq (McPherson, Hormozdiari, Zayed, et al. 2011). Finally, for the purposes of gene prediction or improving existing gene predictions, RNA-seq is a valuable method (Stanke and Morgenstern 2005). In order to learn more about how to implement these, it is recommended that you go through the tutorials of the cited tools.


Anders, Reyes, and Huber. 2012. “Detecting Differential Usage of Exons from RNA-Seq Data.” Genome Research 22 (10): 2008–17. https://doi.org/10.1101/gr.133744.111.

McKenna, Hanna, Banks, et al. 2010. “The Genome Analysis Toolkit: A MapReduce Framework for Analyzing Next-Generation DNA Sequencing Data.” Genome Research 20 (9): 1297–1303. https://doi.org/10.1101/gr.107524.110.

McPherson, Hormozdiari, Zayed, et al. 2011. “deFuse: An Algorithm for Gene Fusion Discovery in Tumor RNA-Seq Data.” PLOS Computational Biology 7 (5): e1001138. https://doi.org/10.1371/journal.pcbi.1001138.

Stanke, and Morgenstern. 2005. “AUGUSTUS: A Web Server for Gene Prediction in Eukaryotes That Allows User-Defined Constraints.” Nucleic Acids Research 33 (Web Server issue): W465–W467. https://doi.org/10.1093/nar/gki458.

Trapnell, Williams, Pertea, Mortazavi, Kwan, Baren, Salzberg, Wold, and Pachter. 2010. “Transcript Assembly and Quantification by RNA-Seq Reveals Unannotated Transcripts and Isoform Switching During Cell Differentiation.” Nature Biotechnology 28 (5): 511–15. https://doi.org/10.1038/nbt.1621.