Deep sequencing of the cancer transcriptome has revealed an unexpected complexity including the presence of proteins that are unique to the cancer. As more than 60% of the genome is now believed to be transcribed, understanding the changes in the coding genes as well as the noncoding regulatory transcriptome is critical for a clear elucidation of the dysfunctional cancer genome. The RNA seq method provides a comprehensive amount of information on the cancer transcriptome: highly sensitive and accurate gene-expression levels, alternative splice forms, novel fusion transcripts, and mutational changes that have a direct impact on protein function. In this webinar, presenters will review transformative discoveries from RNA-seq, and describe a highly effective approach for isolation and characterization of circulating tumor cells using RNA-seq at single cell resolution. Parameters that affect quantification of expressed nucleotide sequence polymorphisms (SNVs) will also be discussed, as will the development and implementation of tools for the identification of fusion transcripts.