Demystifying emerging bulk RNA-Seq applications: the application and utility of bioinformatic methodology

Significant innovations in next-generation sequencing techniques and bioinformatics tools have impacted our appreciation and understanding of RNA. Practical RNA sequencing (RNA-Seq) applications have evolved in conjunction with sequence technology and bioinformatic tools advances. In most projects, bulk RNA-Seq data is used to measure gene expression patterns, isoform expression, alternative splicing and single-nucleotide polymorphisms. However, RNA-Seq holds far more hidden biological information including details of copy number alteration, microbial contamination, transposable elements, cell type (deconvolution) and the presence of neoantigens. Recent novel and advanced bioinformatic algorithms developed the capacity to retrieve this information from bulk RNA-Seq data, thus broadening its scope. The focus of this review is to comprehend the emerging bulk RNA-Seq-based analyses, emphasizing less familiar and underused applications. In doing so, we highlight the power of bulk RNA-Seq in providing biological insights.

Automated summary

Innovations in next-generation sequencing techniques and bioinformatics tools have revolutionized our understanding of RNA. Bulk RNA-Seq data is commonly used to study gene expression, isoform expression, alternative splicing, and more, with hidden biological information such as copy number alterations and presence of neoantigens also being extracted. Advanced bioinformatic algorithms have expanded the capacity to retrieve this hidden biological information, positioning bulk RNA-Seq as a powerful tool for providing biological insights.