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.

Here we explained this in a review published in BIB.

https://ro.uow.edu.au/test2021/3578/

https://academic.oup.com/bib/article/22/6/bbab259/6330938

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