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IM-Fusion

IM-Fusion is a tool for identifying transposon insertion sites in insertional mutagenesis screens using single- and paired-end RNA-sequencing data. It essentially identifies insertion sites from gene-transposon fusions in the RNA-sequencing data, which represent splicing events between the transposon and endogeneous genes.

IM-Fusion also identifies candidate genes for a given screen using a statistical test (based on the Poisson distribution) that identifies Commonly Targeted Genes (CTGs) – genes that are more frequently affected by insertions than would be expected by chance. To futher narrow down a list of CTGs, which may contain hundreds of genes, IM-Fusion also tests if insertions in a CTG have a significant effect on the expression of the gene, which is a strong indicator of them having an actual biological effect.

IM-Fusion has the following key features:

• It identifies transposon insertion sites from both single- and paired-end RNA-sequencing data, without having any special sequencing requirements.
• Its gene-centric approach – both in the identification of insertions and in testing for differential expression of identified candidate genes – greatly reduces the number of false positive candidate genes.
• Its differential expression tests provide detailed insight into the effects of insertions on the expression of their target gene(s). By providing both a groupwise and a single-sample version of the test, IM-Fusion can identify effects for a single insertion in a specific sample, or determine the general effect of insertions on a given gene within the tumor cohort.

For more details on the approach and a comparison with existing DNA-sequencing approaches, please see our paper “Identifying transposon insertions and their effects from RNA-sequencing data” (submitted).

Where to start?

For details on installing IM-Fusion and its dependencies, see Installation.

The main interface of IM-Fusion is its command-line interface, which provides various commands for performing each step of its analysis. For an overview of the analysis and for a guide to preparing the required input files, see Getting started. For more details on the different options available for each command, see Command-line usage.

An API interface is also provided for programmatic use of IM-Fusions various steps, or for creating custom pipelines based on our code. For details on the provided functions, see the API documentation.

Sources

The source code of IM-Fusion is available on Github in the repository jrderuiter/im-fusion. Any questions or issues should also be addressed there.

License

IM-Fusion is released under the MIT license.