How to analyse gene fusion data from RNA seq of a wild type tissue?

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Amir Vajdi

I assume you have a human sample. Then you still can call for fusion from WT RNA-Seq data using STAR Fusion or other methods. However, there is a high chance you'll get some False Positive (FP) calls. Therefore, it's highly recommended to annotate that with some fusion databases.

Here is an example data base which you can put your fusion calls and it tries to find any matches with existing databases.

https://fusionhub.persistent.co.in

Tommaso Mazza

STAR-Fusion, Arriba and STAR-SEQR seem to be the best performers by this publication: https://genomebiology.biomedcentral.com/articles/10.1186/s13059-019-1842-9

I've personally used the latter through Docker and it works easily as a charm.

STAR-Fusion and Arriba have both Docker amd Singularity images available.

Curiously, all three software base on STAR