- Unique identifier:
- Command line interface
- Input format:
- Operating system:
- Unix/Linux, Mac OS, Windows
- GNU General Public License version 3.0
- Bowtie; Perl Modules: Bio::Perl, Bio::Tools::Run::Alignment::Muscle, Getopt::Long, List::MoreUtils, Pod::Usage, Config::IniFiles, Sort::ArrayOfArrays, Term::ProgressBar, GD::Graph, DBI, DBD::mysql; Ensembl API; Muscle; MySQL; Ensembl Database
- Software type:
- Restrictions to use:
- Output data:
- A summary file, which contains a ranked list of fusion candidates based on their evidence strength, a file containing the full details for each isoform of G1 and G2 and the genomic coordinates of the alignment blocks on G1 and G2, with their respective corresponding Ensembl exon IDs, a file that contains a flag denoting the stage at which each read was filtered and statistics detailing the raw numbers of reads that have been filtered at various stages of the algorithm.
- Programming languages:
- Computer skills:
- Richard Francis <>
- FusionFinder Team <>
When I run Fusionfinder, got an error.
Finding gene fusions at Fri Jul 24 13:18:30 2015
Analysis commenced at Fri Jul 24 13:18:30 2015
Processing pseudopairs file: 0% [= ]ETA ------Can't call method "fetch_by_source_stable_id" on an undefined value at ../bin/fusionfinder.pl line 1121, <IN> line 4.
What is this error ?? PLease suggest me a solution.
(Francis et al., 2012)
FusionFinder: a software tool to identify expressed gene fusion candidates from RNA-Seq data.
PMID: 22761941 DOI: 10.1371/journal.pone.0039987
Division of Bioinformatics and Biostatistics, Telethon Institute for Child Health Research, Centre for Child Health Research, The University of Western Australia, Perth, WA, Australia; Division of Children’s Leukaemia and Cancer Research, Telethon Institute for Child Health Research, Centre for Child Health Research, The University of Western Australia, Perth, WA, Australia
Supported by the WA State Government Centres of Excellence Program, the Children’s Leukaemia and Cancer Research Foundation, Perth and the Mike Schon-Hegrad Memorial Fund.
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