Fig. 1. Long-read nanopore sequencing and FLAIR analysis to identify full-length transcripts associated with SF3B1 mutation in chronic lymphocytic leukemia.

a RNA from primary samples across three conditions (chronic lymphocytic leukemia with and without SF3B1 mutation and normal B cells) were obtained. The RNA was prepared into 1D cDNA libraries and each sample was sequenced on a PromethION flow cell. The basecalled data were processed using the FLAIR pipeline. b The FLAIR pipeline constructs an isoform set from nanopore reads. First, reads are aligned to the genome with a spliced aligner. The sequence errors are marked in red. Next, they are splice-corrected using splice sites from either annotated introns, introns from short-read data, or both. The corrected reads are grouped by their splice junction chains and are summarized into representative isoforms (first-pass set). All reads are then reassigned to a first-pass isoform. The isoforms that surpass a supporting read threshold of 3 comprise the final high-confidence isoform set.