RNA-seq analysis workflow. Left panel (1) represents the raw gene expression quantification workflow. Every box contains the algorithms and methods used for the RNA-seq analysis at trimming, alignment, counting, normalization and pseudoalignment levels. The right panel (2) represents the algorithms used for the differential gene expression quantification. *HTSeq was performed in two modes: union and intersection-strict. **EdgeR exact test, edgeR GLM and NOISeq have internally three normalization techniques that were evaluated separately.