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STAR fusion detection is performed in two steps: chimeric alignment of reads with the STAR aligner and fusion detection with STAR-Fusion. Performing fusion detection in two steps is equivalent to running the analysis in "Kickstart" mode, as described by the authors of STAR-Fusion. We recommend using STAR version 2.7.8a (see Task management to check which version you are running).

To save time, you can import the pre-built STAR-Fusion pipeline from our hosted pipeline page. This pipeline includes the two steps outlined below, where the advanced options for the STAR 2.7.8a alignment have been optimized for fusion detection according to the STAR-Fusion author's recommendations. See Importing a Pipeline for more information.

Running STAR Chimeric Alignment within Partek Flow

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