Fig. 5
From: Yanagi: Fast and interpretable segment-based alternative splicing and gene expression analysis
This diagram illustrates a problem with transcript-based approaches for calculating PSI in the presence of unannotated transcripts. (Left) shows the truth, with three isoforms combining two exon skipping events (E1, E2). However, isoform 3 is missing from the annotation. Reads spanning both events are shown along their true source. Reads spanning an exon incluion are colored green whereas reads spanning a skipping junction are colored orange. (Right) shows the problem with PSI values from transcript abundance. Because these two alternative splicing events are coupled in the annotation, their PSI values calculated from transcript abundances will always be the same (\(\psi ^{TPM}_{1}\) = \(\psi ^{TPM}_{2}\)), even though the true values are not (Trueψ1≠Trueψ2). Furthermore, changes in the estimated abundances (TPM1,TPM2) make the calculated PSI values unpredictable. Count-based PSI values (\(\psi ^{C}_{1}, \psi ^{C}_{2}\)) on the other hand correctly reflect the truth