Bioinformatics Seminar
Time: 11AM
Venue: Davis Auditorium and Online
3 December 2024
This is a WEHI only event.Benchmarking long-read RNA-sequencing technologies with LongBench
Yupei YouWEHI Epigenetics and Development
Long-read RNA-sequencing technologies offer unparalleled insights into transcriptomes by enabling full-length sequencing of RNA molecules. With the rapid evolution of long-read RNA-sequencing protocols and bioinformatics tools, the trade-offs between sequencing throughput, read length, accuracy, and cost present significant challenges in selecting the optimal approach. Benchmarking studies that compare these options are crucial to inform future research directions. However, many existing benchmarking datasets with matched data across multiple platforms have limitations, including: 1) a lack of realistic biological replicates, which may restrict the generalisability of differential analysis results to real-world scenarios, and 2) the use of earlier sequencing kits, which may not reflect the latest advancements in sequencing technology. This talk will introduce LongBench, a comprehensive benchmarking dataset designed to fill these critical gaps. Derived from eight lung cancer cell lines with synthetic RNA spike-ins, LongBench includes bulk, single-cell, and single-nucleus RNA-sequencing data from three state-of-the-art long-read sequencing platforms - ONT PCR-cDNA, ONT direct RNA, PacBio Kinnex - alongside Illumina short-read data for robust cross-platform comparisons. With the dataset we present a systematic evaluation of transcript capture, quantification, and differential expression analyses, examining the strengths and limitations of each sequencing platform.