Fig. 1
Overview of SUPPA2 differential splicing and time benchmarking analysis. a The central panel displays the ΔPSI values between replicates (y-axis) as a function of the average transcript abundance (x-axis), using data from [17] (“Methods”). The attached panels display the ΔPSI values along the x-axis (top panel) and along the y-axis (right panel). The green dot represents an example of ΔPSI observed between conditions. The top-right panel shows the between-replicate |ΔPSI| density distribution against which an observed |ΔPSI| is compared to obtain a p value. This density distribution is calculated from events with similar associated expression. b The central panel displays the ΔPSI values (y-axis) between conditions (green) or between replicates (gray) as a function of the average transcript abundance (x-axis) in log10(TPM + 0.01) scale. Only events with p value < 0.05 according to SUPPA2 are plotted in green. The attached panels display the distribution of the significant ΔPSI values along the x-axis (top panel) and along the y-axis (right panel). c Time performance of SUPPA2 compared to rMATS, MAJIQ, and DEXSeq in the differential splicing analysis between two conditions, with three replicates each [17]. Time (y-axis) is given in minutes and in each case it does not include the read mapping, transcript quantification steps, or the calculation of PSI values