Fig. 3From: Bridging the gap between reference and real transcriptomesRNA-seq pipelines for the discovery and quantification of transcripts and processing events, unconstrained by a RefT. Software in black are best suited to “small” input datasets (represented by an arbitrary size N < 20) while software in blue can process large datasets (up to hundreds of libraries). Protocols are subdivided into four combinations of genome-guided versus de novo and assembly-based versus local event discovery. Local events include splice variants, transcribed regions, gene fusions, circular RNAs, sequence polymorphisms (SNV) and expressed transposons (Additional file 1: Table S2). Results from assembly software can be used as RefTs in standard quantification pipelines (inset)Back to article page