SPOP and breast carcinoma: The five best-in-class RNA-seq pipelines compared here produce consistent results for nearly 88% of protein-coding genes, including many disease-associated genes, such as genes associated with breast cancer (BRCA1, TP53, and ERRB220, Supplementary Fig. S11), prostate cancer (SPOP, IDH1, AKT121, Supplementary Fig. S12), and glioblastoma (SPOP, IDH1, AKT122, Supplementary Fig. S13).