FusionQ is a novel fusion detection tool based on paired-end RNA-Seq data. This tool can detect gene fusions, construct the structures of chimerical transcripts, and estimate their abundances. This tool employs a new approach, "residual sequence extension", which extends the short segments of the reads by aggregating their overlapping reads. A list of filters are proposed to control the false-positive rate. 

  • Download and install boost thread (1.42.0 and above):
  • Download and install R:
    • http://cran.r-project.org/
  • Download and intall Perl:
  • Download and install SAMtools: 
    • http://samtools.sourceforge.net/
Please make sure that above programs are included in your PATH.
Please make sure the above two programs are placed in the script folder.

About boost:
      if boost is installed locally, please do the following before installation:
       export BOOST_DIR  


FusionQ is freely available at https://sites.google.com/site/fusionq1/home/download    

Getting Started

  • Once you download FusionQ at the download page, please extract FusionQ as follows:
    •   tar zxvf FusionQ.tar.gz
  • You will find two folders under FusionQ: FusionQ_code, script. Move the script folder and source code folder to your favorite location. Go to the FusionQ_code folder, and make:
    • cd /path/to/FusionQ_code
    • make
  • To test the installation,
    1. Download the test_data.tar.gz in the download page, and extract the folder. tar jxf test_data.tar.gz
    2. Download the genome reference files: genes.gtf, genome.fa,refGene.txt through http://cufflinks.cbcb.umd.edu/igenomes.html Homo_sapiens_Ensembl_GRCh37.
    3. Place them in test_data/Process/Database/Ensembl/
    4. test_data/run.sh
  • In the installation is successful, you can start to use FusionQ as follows:
    1. Modify the configuration file of run.sh and run.cfg in the script folder. 
      • Examples of these two files can be found in test_data/run.cfg and test_data/run.sh.
    1. Execute FusionQ
      • /path/to/run.sh

output file folder is sepecified in the run.cfg file:  out_path. Four files are used to profile the detected fusions, including: 
  • fusion_gene_results
  • fusion_isoform_results
  • fusion_seq.txt
  • fusion_supporting_reads.txt

  • In order to unintall FusionQ, simply go to the executive file folder, and uninstall it by:
    •   cd /path/to/FusionQ
    •   make clean

  • About the transcriptome construction.
           We construct transcriptome  based on Cufflinks. When I use cufflinks, the parameter added is –g, which will includes all known transcripts as well as novel transcripts ( a more complete library).
              If you would like only the FusionQ involving known transcripts, please use parameter –G.
              If you would like a small library ( which makes the following computation faster), please do not add either of these two parameters.
  •     System Problem:
                 Thanks for all who gave us kind feedback and suggestions. In version 1.0, I didn't try on Ubuntu 64, it might be a problem when using Ubuntu 64. 
                  I modified the Makefile according to the suggestion in the feedback, but it still not successful for all Ubuntu 64 system. I'm trying it fix it out now.

  •     Liu C, Ma J, Chang C, Zhou X: 
    FusionQ: a novel approach for gene fusion detection and quantification from 
    paired-end RNA-Seq. BMC Bioinformatics 2013, 14:193 doi:10.1186/1471-2105-14-193

  • Li B, Dewey C: RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. BMC Bioinformatics 2011, 12(1):323. 
  • Rice P, Longden I, Bleasby A: EMBOSS: The European Molecular Biology Open Software Suite. Trends Genet 2000, 16(6):276–277.
  • Li H, Ruan J, Durbin R: Mapping short DNA sequencing reads and calling variants using mapping quality scores. Genome Res 2008, 18(11):1851–1858.  

  •    Please email the author for any questions.

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