Subsections


Output from the Detect and Refine Fusion Genes tool

The Detect and Refine Fusion Genes tool produces a number of outputs:

  1. Fusion Genes (WT): The Fusion Genes track contains the breakpoints of all detected fusions. The track is described in more details below, see 31.4.2.
  2. Reads (WT): A read mapping to the WT genome. Reads are mapped to a combination of the WT genome and the artificial fusion chromosomes. Reads mapping better to the artificial fusion chromosomes will be in the Reads (fusions) output.
  3. Unaligned Ends: A read mapping showing where the unaligned ends map to the reference genome. The unaligned ends track is useful when choosing how to set the parameters "Minimum unaligned end 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. Note that the unaligned reads are mapped using RNA-Seq Analysis default parameters allowing a maximum of 10 hits per read.
  4. Fusion Genes (fusions): Breakpoints for the detected fusions on the artificial reference.
  5. Reads (fusions): A read mapping to the artificial fusion chromosomes. Reads are mapped to a combination of the WT genome and the artificial fusion chromosomes. Reads mapping better to WT genome will be in the Reads (WT) output.
  6. Reference Sequence (fusions): Reference sequence for the artificial reference.
  7. mRNA (fusions): mRNA transcripts corresponding to the detected fusions on the artificial reference.
  8. Genes (fusions): Gene region for the fused gene product on the artificial reference.
  9. CDS (fusions): If the CDS track was provided, this track contains the CDS region for the fused gene product on the artificial reference.
  10. Primers (fusions): If a primer track was provided, this track contains the primer regions on the artifical reference. Note that only primers for genes involved in a detected fusion will be represented here, and that the same primer can be in multiple fusion chromosomes, if the the same gene is involved in multiple fusions.
  11. Report: A report containing graphical representations of the fusions passing all filters. The report is described in more detail below, see 31.4.2.

Fusion tracks

The fusion track has a table view describing the fusions or exon skipping events on multiple lines, with two lines for each breakpoint that was detected. It contains the following information:

Detect and Refine Fusion Genes report

In the Result handling dialog, it is possible to choose to output a report containing sample and unaligned ends information as well as detailed information and plots for all fusions passing filters (figure 31.55):

The report has three sections: "Summary", "Unaligned Ends" and "Fusions". The summary section has a table with the sample name. The unaligned ends section contains a table with statistics on the unaligned ends used to detect fusions, the table has the following information:

Image detect_and_refine_report_unaligned_ends
Figure 31.58: Unaligned ends section in Detect and Refine Fusion Genes report.

The Fusion section lists all fusions with FILTER=PASS. Each Fusion Gene is described by two tables and a fusion plot (figure 31.56).

Image refinefusionreport
Figure 31.59: A report section for a fusion gene.

The first table contains an overview of the most supported fusion for the fusion gene. Values in this table include:

The second table lists values for all supported fusion breakpoints in the fusion gene, sorted by read count. Therefore the first row in the table recapitulates some of the values from the first table. Additional rows show evidence for other fusions between the same two genes. At most 10 rows are shown.

The fusion plot visualizes all fusions between the reported transcripts.

Known limitations