Detect Fusion Genes

This tool has been deprecated and will be retired in a future version of the software. It has been moved to the Legacy Tools (Image legacy_tools) folder of the Toolbox, and its name has "(legacy)" appended to it. If you have concerns about the future retirement of this tool, please contact QIAGEN Bioinformatics Support team at

Detect Fusion Genes is designed to find candidate fusion genes that should typically be investigated further by Refine Fusion Genes, described in Refine Fusion Genes. This tool is generally not run in isolation.

Briefly, the tool works by re-mapping the unaligned ends of reads and determining if these are consistent with a fusion. Fusions are identified from reads that must have an unaligned end close to an exon boundary that can be remapped close to another exon boundary. If the option for Detect fusions with novel exon boundaries has been enabled, the tool also considers reads that are far from an exon boundary and/or whose unaligned ends can be mapped far from an exon boundary in a second pass.

The Detect Fusion Genes tool can be found in the Toolbox at:

        Tools | QIAseq Panel Expert Tools (Image qiaseq_expert_folder_closed_16_n_p) | QIAseq RNAscan Panel Expert Tools (Image fusion_gene_detection_folder_closed_16_n_p) | Detect Fusion Genes (Image find_fusions_16_n_p)

The Detect Fusion Genes tool takes an RNA-seq read mapping as input (figure 26.1).

Image findfusion1
Figure 26.1: Select an RNA-seq read mapping.

In the next dialog figure 26.2, specify the reference sequence, gene and mRNA track from the CLC_References folder of the Navigation Area. It is possible - but optional - to add a CDS or primer track to run the analysis.

Image findfusion2
Figure 26.2: Specify references and parameters for the detection.

The additional parameters to set are:

In the Result handling dialog, it is possible to choose to output a report with unaligned ends information (figure 26.3):

This report can be used together with the Combine Reports tool (see

Image findfusion3
Figure 26.3: Unaligned ends report.

Known limitations

Detect Fusion Genes otherwise generates a read mapping, an unaligned ends track, a fusion track (see the details of the fusion track in Fusion tracks, and several tracks for use in Refine Fusion Genes. The unaligned ends track is useful when choosing how to set the parameters "Minimum fusion read count", "Minimum length of unaligned sequence", and "Maximum distance to exon boundary" for a particular panel and sequencing protocol in order to find known fusions, as it shows which unaligned ends of reads were considered and where they were mapped.