Comparison of the DG-seq and ViReMa pipelines. (A) RNA-seq data corresponding to RT-seq and RT-PCR-seq on the WT, PA-K635A, and PA-R638A viral stocks from Expt 1 were analyzed using the ViReMa pipeline. For each sample, DVGs identified upon DG-seq analysis were compared to DVGs detected with the ViReMa pipeline. The percentage of PA, PB1, and PB2 DVGs detected with DG-seq with respect to (wrt) ViReMa (left panel) and conversely (right panel) are shown. The comparison was made using background thresholds specific for each pipeline (read counts ≥14 for DG-seq; ≥30 (PA) or 20 (PB1, PB2) for ViReMa). (B) RNA-seq data corresponding to RT-seq and RT-PCR-seq on the mixes of in vitro transcribed vRNAs spiked with pseudo-DVGs at frequencies of 0.5, 0.1, 0.01, or 0.001 (as described in Fig. 3) were analyzed using the ViReMa pipeline. The read counts of each synthetic pseudo-DVG obtained with ViReMa is plotted against the DG-seq read counts. The background thresholds specific for each pipeline are indicated by dotted lines (read counts ≥14 for DG-seq; ≥20 for ViReMa). (UD) Undetected.
