FLAIR2 results from Oxford Nanopore sequencing of R2C2 libraries generated from Human WTC11 and Mouse ES cell lines from the Long-read RNA-seq Genome Annotation Assessment Project (LRGASP) (Pardo-Palacios et al. Nature Methods 2024). FLAIR2 high-confidence isoforms are provided for WTC11 and ES cells. For Mouse ES cells, sequence variants were identified with Longshot and incorporated into transcript isoforms using FLAIR2. These data are associated with the FLAIR2 publication (Tang et al. 2024)