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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.