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 |