Fig. 5: Identification of SNV-associated differential transcript structures.
From: Single-cell long-read targeted sequencing reveals transcriptional variation in ovarian cancer
a Workflow for detecting SNV-associated differential transcript structures: (i) Obtain reads from ovarian tumor epithelial cells (scTaILoR-seq), (ii) Determine SNVs using Clair3, (iii) Predict cryptic splice events using SpliceAI, (iv) Compute coverage divergence between reference (REF) or alternative (ALT) variant reads, (v) Identify differential transcript structures among SpliceAI hits using coverage divergence. b SNVs of genes exhibiting SpliceAI score above the threshold value of 0.1. Each SNV is colored by SpliceAI score and whether a hit also displays coverage divergence between REF and ALT. c Hierarchical clustering based on extent of divergence at transcript structural elements (CDS and UTR/Intron) of 44 “Hit and divergent” SNVs. d, e Plots for ELF3 and STAT1, respectively: normalized coverage tracks for REF and ALT and corresponding transcript model. Source data are provided as a Source Data file.
