Knowledge Exchange: cDNA Sequencing with nanopore technology

In this Knowledge Exchange Phill James and Botond Sipos discuss Oxford Nanopore cDNA sequencing kits which aim to allow the comprehensive analysis of transcriptomes using long-read sequencing. They'll explore the mechanics and applications for both the PCR based approach (PCS-109) and a PCR free or “direct” cDNA sequencing kit (DCS-109).

The first half of the Knowledge Exchange aims to help the user determine which approach is best suited to the application of choice from a lab users’ perspective, with detailed explanations of how each kit works at the molecular level, pros and cons of each approach, expected data outputs, and tips and tricks to get the most of your sequencing run. Using examples of real data sets generated by these two methods, the second half of this Knowledge Exchange will delve into the data analysis side of cDNA sequencing. From pipelines and analysis approaches developed by the Nanopore Community and Oxford Nanopore’s in-house bioinformaticians, the primary focus of this section is how to get the most from your raw cDNA sequencing reads, including isoform reconstruction, differential gene expression, and differential isoform usage.