Fig. 1.

Flow diagram as provided by AutoFlow for the detection of RGs using the SRA datasets of PRJEB9470 from Arabidopsis. a The first workflow that prepares the reads, maps them on the transcriptome and provides the read count table. b The findRGs workflow for detecting candidate RGs. In this example, several filtering parameters were tested: 10 and 20% for the maximum CV, and 10,000, 30,000 and 100,000 reads for the minimum counted reads per transcript and condition. One Venn diagram by each CV cut-off is obtained, as shown in Figs. 2, 4, 5 and 6