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Table 1 Gene selection options in FUSIM

From: FUSIM: a software tool for simulating fusion transcripts

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
  1. Gene selection modes and corresponding options in FUSIM.