Characterization of full-length isoforms in single cells with nanopore long-read sequencing

Luyi Tian from Walter and Eliza Hall Institute of Medical Research, Australia discusses Full-length transcriptome sequencing (FLT-Seq) and new toolbox FLAMES (full-length analysis of mutation and splicing) for the characterization of full-length isoforms in single cells with nanopore long-read sequencing
FTL-Seq couples the 10x scRNA seq protocol with Nanopore long-read sequencing and can be conducted on multiple different cell types, cell lines and frozen patient samples. FLAMES is used to detect and quantify known and new isoforms and outperformed short-read methods in combination with TALON, FLAIR and StringTie in both isoform detection and quantification with similar sequencing depth.
‘Characterization of isoforms showed nearly half of the Isoforms detected in the pipeline are not present within a known isoform’ which lead to Luyi conducting differential transcript usage analysis and identified different isoforms within different cells were a result of a different transcription start sites (TSS) which corresponded to different open chromatin regions.