...

The reads are first aligned to the genome and initially , unaligned reads are then split into multiple 25 bp sequences which are, in turn, aligned to the genome by Bowtie. TopHat-Fusion algorithm then identifies the cases where the first and the last 25 bp segment are aligned to either two different chromosomes or two locations on the same chromosome (spacing is defined by the user). The whole read is then used to identify a fusion point. After the initial fusion candidates are defined, all the segments from initially unaligned reads are realigned against the fusion points (as well as intron boundaries and indels) and the resulting alignments are combined to full read alignments.

The most up to date TopHat-Fusion version implemented in Partek Flow when the manual was written (2.1.0) focuses on fusions due to chromosomal rearrangements, while fusions resulting from read-through transcription or trans-splicing were not supported. TopHat-Fusion can handle both paired- and single-end reads, but the support of color-space reads is still pending. For details as well as discussion of TopHat-Fusion options, see TopHat-Fusion home page (4).

...

The list of annotated fusion genes, in a form of Fusion report (Figure 117), can be obtained by first selecting the Fusion report task node and then the Task report link from the toolbox. Each row of the table in Figure 7 is a potential fusion event, with the columns providing the following information.

• Sample ID: sample in which the fusion event was identified;
• Chromosome 1: chromosome hosting the first (left) segment of the fusion transcript;
• Stop 1: end of the first (left) segment of the fusion transcript;
• Chromosome 2: chromosome hosting the second (right) part of the fusion transcript;
• Start 2: beginning of the second (right) segment of the fusion transcript;
• Gene1: gene on the left side of the fusion;
• Gene2: gene on the right side of the fusion;
• Spanning reads: number of reads which were unaligned during the initial phase of TopHat and where only one mate is used as evidence of the fusion event;
• Mate Pairs: number of reads which were unaligned during the initial phase of TopHat and where both mates are used as evidence of the fusion event;
• Spanning mate pairs: number of reads where both mates were aligned during the initial phase of TopHat, but their pairing is discordant (e.g. different chromosomes, different orientation etc.);
• Contradicting reads: number of reads which do not support the fusion;
• Left bases: number of bases on the left side of the fusion;
• Right bases: number of bases on the right side of the fusion.
  
  

All the columns can be sorted by using the arrow buttons in column headers, while the type-in boxes can be used for searching. TopHat-Fusion does not report exact start and stop position for each side of the fusion event. It has a single location for the end of the upstream segment (Stop 1) and the beginning of the downstream segment (Start 2). Columns Therefore, columns Start 1 and Stop 2 are added for (internal) consistency with other Partek Flow tools.

...

STAR fusion detection algorithm is integrated with STAR aligner and fusion detection is activated by tick-marking Chimeric alignment option in the Advanced options of the aligner (the Advanced options dialog is reached via Configure link in the setup dialog). As soon as the Chimeric alignment is selected, additional options, specific to the fusion search algorithm, are shown (Figure 1511). For discussion on the options details, see STAR documentation.

...

The output is associated with the Chimeric results data node (Figure 1612), which is a part of STAR results (in addition to Aligned reads node and, optionally, Unaligned reads node).

...

Selecting the Chimeric results node opens the toolbox (Figure 1713) with twooptions: Data summary report or Download data.

...

Clicking on the Download data results in download of a .fusion file to the local computer. The file is human readible and can be opened in a text editor (example in Figure 1814). For details refer to STAR's documentation.

...