Longer read lengths are required for RNA velocity analysis of single-cell RNA-sequencing with paired immune repertoire and transcriptome profiling

Increasing numbers of studies utilize single cell sequencing (scSeq) technologies that are capable of simultaneously profiling T/B-cell receptor (TCR/BCR) sequences and RNA expression. Here we show that standard sequencing of commonly-used 5'-biased scSeq chemistry precludes the ability to perform RNA velocity analysis; however extended sequencing lengths that allow for paired-end genome alignment alleviates these issues. This study provides important practical implications for paired TCR/BCR and RNA scSeq experiments. Overall design: Single-cell RNA-sequencing of untreated human triple negative breast cancer samples (n = 5 patients) enriched for CD45+ cells.