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.
Requirements
- Download and install boost thread (1.42.0 and above):
- http://cran.r-project.org/
- Download and intall Perl:
- Download Bowtie, Cufflinks
- Download and install SAMtools:
- http://samtools.sourceforge.net/
Please make sure that above programs are included in your PATH.- EMBOSS (One version has been placed in the script folder):
- RSEM (One version has been placed in the script folder):
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: BOOST_DIR=/path/to/boost export BOOST_DIR
- Once you download FusionQ at the download page, please extract FusionQ as follows:
- 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,
- Download the test_data.tar.gz in the download page, and extract the folder. tar jxf test_data.tar.gz
- Download the genome reference files: genes.gtf, genome.fa,refGene.txt through http://cufflinks.cbcb.umd.edu/igenomes.html Homo_sapiens_Ensembl_GRCh37.
- Place them in test_data/Process/Database/Ensembl/
- test_data/run.sh
- In the installation is successful, you can start to use FusionQ as follows:
- 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.
- Execute FusionQ
Outputoutput 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
Uninstall- In order to unintall FusionQ, simply go to the executive file folder, and uninstall it by:
- cd /path/to/FusionQ
- make clean
Questions: - 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. 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.
Publication- 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
Reference- 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.
Contact- Please email the author for any questions.
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