a software tool for simulating fusion transcripts

Introduction

FUSIM is a tool for simulating fusion transcripts. Multiple types of fusion transcripts are supported and based on the number of genes involved per fusion, the fusion types are classified as self, hybrid, complex which involves 1, 2, and 3 genes respectively. According to chromosome locations and strand, fusion types are classified as CTX (inter-chromosome events), ITX (intra-chromsome events with different strands), DUP (tandem duplication), and DEL (deletion). Complex chromosomal rearrangements (CCRs) are examples of complex fusions involving at least three breakpoints on two or more chromosomes. Read through events are also supported as a special case of DEL with two adjacent genes on the same strand fused together. See the figure below which shows how fusion transcripts are generated:

User Guide

Basic Usage

Show all available options:
```
$ java -jar fusim.jar -h
```

Generate fusion transcripts:

$ java -jar fusim.jar --gene-model refFlat.txt --fusions 10

Output to both FASTA and TXT format:

# Be sure your reference genome is indexed using samtools
$ samtools faidx hg19.fa

$ java -jar fusim.jar \
     --gene-model=refFlat.txt \
     --fusions=10 \
     --reference=hg19.fa \
     --fasta-output=fusions.fasta \
     --text-output=fusions.txt

Use background dataset

Generate Fusion transcripts based on a background dataset (BAM file) using RPKM cutoff of 0.2. Note background BAM files must be indexed (*.bam.bai):

# Be sure to index your BAM file first
$ samtools index myreads.bam

$ java -jar fusim.jar \
     --gene-model=refFlat.txt \
     --fusions=10 \
     --background-reads=myreads.bam \
     --rpkm-cutoff=0.2

Filtering Options

FUSIM has the ability to limit simulated fusion transcript to specific genes or chromosomes of interest. To filter simualted transcripts:

$ java -jar fusim.jar \
     --gene-model=refFlat.txt \
     --fusions=10 \
     --gene1=BCR \
     --gene2=ABL1

Filter by multiple genes:

$ java -jar fusim.jar \
     --gene-model=refFlat.txt \
     --fusions=10 \
     --gene1=BCR,NPS \
     --gene2=ABL1,RPL38

Gene Selection Options

Mode

Method

Options

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
empirical
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