Table 1.

Gene selection options in FUSIM

Mode	Method	Options	Description
Random (default)	uniform	‐l,‐limit	Limit all fusions to specific geneId, transcriptId, or chrom
		‐1,‐gene1	Filter for gene1
		‐2,‐gene2	Filter for gene2
		‐3,‐gene3	Filter for gene3
Background	uniform emprical binned	‐b,‐background‐reads	Path to BAM file containing background reads. Genes will be selected for fusions according to the read profile of the background reads
		‐k,‐rpkm‐cutoff	RPKM cutoff when using background BAM file. Genes below the cutoff will be ignored
		‐m,‐gene‐selection‐method	Method to use when selecting genes for fusions uniform|empirical|binned
		‐p,‐threads	Number of threads to spawn when processing background BAM file

Gene selection modes and corresponding options in FUSIM.