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Fusion report displays an annotated report on detected fusion genes. For that purpose, an annotation file needs to be specified first (Figure 18).

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All the columns can be sorted by using the arrow buttons () in column headers.

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Moreover, Fusion attribute report, when invoked from the Chimeric results node, displays a report on attributes of detected fusion genes. Attributes to be tested for association with the fusion should be specified (Figure 21).

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A new data node, Fusion attribute report, is generated in the Analysis tab (Figure 22) and it provides access to the Task report link in the toolbox.

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The output, Fusion report table (Figure 23) resembles the basic TopHat-Fusion output (Figure 11); each row of the table is a single fusion events and event and three right-most columns are as follows:

• p-value: p-value for the chi-squared test comparing the observed number of counts against across the levels of the attribute specified in the setup;
• % in (attribute level): fraction of reads detected within the samples belonging to the specified level of the attribute (each level is presented as a single column).

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   1. Costa V, Aprile M, Esposito R, Ciccodicola A. RNA-Seq and human complex diseases: recent accomplishments and future perspectives. Eur J Hum Genet. 2013;21:134-142.
   2. Kim D, Salzberg SL. TopHat-Fusion: an algorithm for discovery of novel fusion transcripts. Genome Biology. 2011;12:R72
   3. TopHat-Fusion. An algorithm for discovery of novel fusion transcripts. http:// http://tophat.cbcb.umd.edu/fusion_index.html Accessed on April 25, 2014
   4. Dobin A, Davies CA, Schlesinger F et al. STAR: ultrafast universal RNA-seq aligner. Bioinformatics. 2013;29:15-21.

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