Michael Nakai from the Peter MacCallum Cancer Centre in Australia spoke at London Calling 2024. The session title was “Isopod: detecting differential isoform usage from long-read single-cell data.” Nakai is a Ph.D. candidate and explained why we are interested in isoforms and splicing events. With long-read sequencing, information about splicing and different isoforms can be obtained. Differential transcript expression (DTE) can be obtained. Nakai then explained differential transcript usage (DTU), which is used to highlight the use of different isoforms. Single-cell datasets in bulk datasets are important. Bulk and single-cell transcript usage has been compared. Nakai and team developed Isopod: an R package for long-read single-cell OTU analysis. This tool uses count data. The first preprocessing step reduces noise. Isopod compares cluster data to other clusters and stores the p-value. This is reproduced ten thousand times with random shuffling. The team is still working on the software package and believes that long-read sequencing can be used for transcript-level detail in single-cell sequencing datasets. DTU analysis can expose isoform-switching events.
