Fig. 1

Annotation and usage of HIV-1 splice sites by ONT sequencing in infected T cells. a Sashimi plots for flanking and alternatively spliced exons determined by ONT sequencing in infected CD4+ T cells from 3 donors were visualized in IGV. Exon boundaries between putative SD and SA sites are symbolized in grey lines. Organization of HIV NL4-3 genome is indicated. b SD (in blue) and SA (in red) sites considered in the rest of the analysis are presented. Enlarged representations allow the observation of previously reported cryptic SS as well as putative new SS (indicated by a black dot). Values represent the sum of reads mapping to each SS across the three T cell samples