What can STAR-Fusion do ?

Question

[tiago211287]

I am trying to understand exactly what can STAR-fusion do, reading the manual I saw that :

STAR-Fusion further processes the output generated by the STAR aligner to map junction reads and spanning reads to a reference annotation set (using a GTF file, ideally the same annotation file used during the STAR genome index building process during the initial STAR setup).

Can someone that uses Star-fusion or already used explain better in what situations is it good for?

[Devon Ryan]

It appears to be doing non-canonical 2-pass splice junction mapping. That's just my reading of it, though, since I've never used it. The paper mentioned on the STAR-fusion page mentions looking for kinase fusions, so that would fit my reading.

[tiago211287]

I am asking because I dont get the difference between the normal splicing indentification by STAR and the junction reads mapping by STAR-fusion.

[Devon Ryan]

The only differences I see are (1) it's two-pass and (2) presumably it does different filtering than the normal --twopass (or whatever it's called) option.

You could ask Alex Dobin for a definitive answer. He's quite good at replying to questions on the STAR forum. In fact, it looks like Brian Haas also replies actively there.

[tiago211287]

That would be nice indeed. Thanks.