RNA-Seq evidence of previously described gene fusions. We first tested our SE approach on (A) the HCC1937 cell line that harbours the fusion NFIA-EHF. SE reads are shown to map across the exon-exon fusion junction between exon 2 of NFIA and exon 5 of EHF, as illustrated in the schematic. Next, we tested our PE approach on (B) two primary tumors that contain ETV6-NTRK3. Results from the sample SEC2 are shown. Paired reads (indicated by two solid lines joined by a dotted line) as well as single reads (red lines) are shown to map across the fusion junction between exon 5 of ETV6 and exon 14 of NTRK3.