Figure 1

Pipeline of the simulation. Simulation workflow used both in Set-up 1 and Set-up 2. Complete annotation (CA) was given to Flux Simulator to generate strand specific PE reads (R). Reads were aligned on the reference genome using TopHat2. TopHat2 was independently used in three different ways (with CA, IA and without annotation). For each execution an alignment bam file was obtained. The alignment bam files were used as input for the compared methods. For each alignment file CEM and Cufflinks were used in Mode 1, 2 and 3; Slide was used in Mode 1 and 2, iReckon was used only in Mode 2. When providing annotation during the alignment, the same annotation was also used for Mode 1 and 2 (see green boxes for CA and pink boxes for IA). When the data driven alignment was carried out we further distinguished (in Mode 1 and 2) the cases with CA and IA, as annotation (see purple boxes). Since RSEM does not work with aligned reads, the output of Flux simulator was processed using CA or IA as annotation (depicted in a green and pink box, respectively).