The occurrence of chimeric transcripts has been reported in many cancer cells and seen as potential biomarkers and therapeutic targets. Modern high-throughput sequencing technologies offer a way to investigate individual chimeric transcripts and the systematic information of associated gene expressions about underlying genome structural variations and genomic interactions. The detection methods of finding chimeric transcripts from massive amount of short read sequence data are discussed here. Both assembly-based and alignment-based methods are used for the investigation of chimeric transcripts.
Chu, H. T. (2016). Transcriptome sequencing for the detection of chimeric transcripts. In Methods in Molecular Biology (Vol. 1381, pp. 239–253). Humana Press Inc. https://doi.org/10.1007/978-1-4939-3204-7_14