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Table 1 The number of fusion genes and breakpoints called in the non-cancer cell line NA12878 from ONT direct RNA and amplified cDNA. Most calls are presumed to be false positives. The number of fusions in the highest rank category for each tool is shown in bold. We hypothesize that most of the multi-read fusions reported by LongGF applied to the cDNA dataset (173) are chimeras introduced during library preparation. JAFFAL ranks these events as Low Confidence. The number of breakpoints for LongGF is not shown as it only reports one breakpoint per fusion gene by default

From: JAFFAL: detecting fusion genes with long-read transcriptome sequencing

 

Direct RNA

cDNA

Total reads processed

14,971,421

25,418,307

 

Fusion genes

Break points

Reads support: median (range)

Fusion genes

Break points

Reads support: median (range)

Fusion genes called by JAFFAL

High confidence

4

4

4.5 (2–14)

8

8

6 (2–24)

Low confidence

5

7

2 (2–11)

94

121

2 (2–49)

Potential trans-splicing

344

344

1 (1–1)

412

412

1 (1–1)

Fusion genes called by longGF

>  1 Read support

5

2 (2–14)

173

2 (2–522)

= 1 Read support

713

1 (1–1)

386

1 (1–1)