FusionCatcher is another option.
FusionCatcher searches for novel/known fusion genes, translocations, and chimeras in RNA-seq data (paired-end reads from Illumina NGS platforms like Solexa and HiSeq) from diseased samples. The aims of FusionCatcher are: very good detection rate for finding candidate fusion genes, very easy to use (i.e. no a priori knowledge of databases and bioinformatics is needed in order to run FusionCatcher), to be as automatic as possible (i.e. the FusionCatcher will choose automatically the best parameters in order to find candidate fusion genes, e.g. finding automatically the adapters, building the exon-exon junctions automatically based on the length of the input reads, etc.) while providing the best possible detection rate for finding fusion genes
Current citation for FusionCatcher:
D. Nicorici, M. Satalan, H. Edgren, S. Kangaspeska, A. Murumagi, O. Kallioniemi, S. Virtanen, O. Kilkku, FusionCatcher - a tool for finding somatic fusion genes in paired-end RNA-sequencing data, bioRxiv, Nov. 2014, DOI:10.1101/011650
A third vote for TopHat-Fusion, I recently used to see fusion in brain cancer samples, it predicts a lots of possible fusion (you can filter the results by coverage and a secondary analysis for mapping specificity with blat).
Is TopHat fusion included in Galaxy Server??
This should probably be asked as a comment on one of the existing answers suggesting tophat-fusion or, since multiple answers suggested tophat-fusion, as a comment to your original question. But, definitely not as an answer to your question.
have you ever used SOAPfuse,can you tell me how to use SOAPfuse?
the details of command.
I had a concern about the outputs from 2 gene fusion calling tools that I was able to get to work. I ran Tophar-fusion and STAR-fusion on one of my RNA-Seq samples and the output gene fusion list doesn't match at all.
Has anyone else faced a similar issue before ? Any thoughts on why this could be the case would be really appreciated.
Thanks a lot.
Please provide more info:
How the output was compared? Have you checked if the output is matched when allowing +/- shift in breakpoint coordinates? Are there any matches if fusion list is collapsed to gene pairs?
What is the average number of fusions you've got with each tool? What about the coverage: number of reads spanning the junction itself, etc?
Are you sure that there are any fusions in your sample? :)
Actually, Tophat-fusion and STAR-fusion need a lot of improvement. Tophat-fusion consistently in is the bottom of all comparisons of fusion finders. TopHat-fusion calls hundreds of thousands of fusions per sample when it is well known that fusions are very rare and one has one fusion for every 10 samples analyzed. Therefore is it is expected that the lists of fusions from TopHat-fusion and STAR-fusion do not match at all.