a software tool for simulating fusion transcripts


Installing Fusim

Fusim is written in Java and requires a working Java runtime version 1.6 or greater

  1. Download Fusim
  2. Unpack the .tar.gz or .zip file as follows:
    $ unzip fusim-X.X.X.zip
    $ cd fusim-X.X.X
  3. Run Fusim:
    $ java -jar fusim.jar --help
    usage: fusim --gene-model=refFlat.txt [options]

Download gene model from UCSC

  1. Download UCSC RefFlat GenePred data:
    $ wget -O refFlat.txt.gz http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/refFlat.txt
    $ gunzip refFlat.txt.gz

Index reference genome file

  1. Download genome reference from UCSC:
    $ wget ftp://hgdownload.cse.ucsc.edu/goldenPath/hg19/bigZips/chromFa.tar.gz
  2. Extract and build one single fasta file:
    $ tar -xzf chromFa.tar.gz
    $ cat chr*.fa > hg19.fa
  3. Index using samtools:
    $ samtools faidx hg19.fa