Abstract Long-read single-cell RNA sequencing enables simultaneous and unbiased detection of transcriptomic variants and gene expression, but its application is limited by low read coverage, restricting genotype-phenotype analyses at single-cell resolution. We systematically evaluate short-read whole-transcriptome amplification (SR-WTA), long-read whole-transcriptome amplification (LR-WTA), and long-read targeted sequencing (LR-Twist). Based on these comparisons, we develop a hybrid strategy combining SR-WTA and LR-Twist within a Snakemake pipeline to leverage the strengths of both approaches. SR-WTA provides broad transcriptome coverage, while LR-Twist enriches a 50-gene panel for deeper variant detection. This approach improves the power to link mutational profiles with transcriptional programs at single-cell resolution.
Wang et al. (Mon,) studied this question.