A comparison of long read single cell transcriptomic approaches

This project benchmarks long-read single-cell RNA sequencing technologies using matched cDNA generated with the 10x Genomics platform. We performed parallel sequencing of the same single-cell cDNA libraries on PacBio and Oxford Nanopore platforms, alongside standard Illumina short-read sequencing as a reference for data quality and transcript recovery. In addition, we evaluated the impact of CRISPR-based depletion of abundant transcripts prior to long-read sequencing to assess whether targeted removal improves transcriptome coverage and isoform representation. By analysing single-source cDNA across platforms, we provide a controlled comparison of long-read performance, examining read- and gene-level metrics, isoform detection, and concordance in clustering and cell type identification relative to the short-read standard. This work establishes a practical benchmarking framework for the optimisation and interpretation of long-read single-cell transcriptomic data