Fig. 1
From: Retained introns in long RNA-seq reads are not reliably detected in sample-matched short reads
Overview of experimental plan. Long- and short-read RNA-seq data from the same biological specimen [47, 48] were downloaded from the SRA and subject to processing and analysis. Short reads (left path) were aligned and quantified according to the requirements of eight short read RI detection tools [37,38,39,40,41], and retained introns were called by each of these. The raw long Iso-Seq reads (right path) were processed to the stage of full-length non-concatemer (FLNC) reads, but left unclustered. After long reads were aligned to the reference genome, each aligned read was assigned to a best match transcript or discarded, and intron persistence was calculated. The called RI output of each short read detection tool was compared against the set of persistent introns identified in the long-read data (where \(P_i \ge 0.1\)). Created with BioRender.com