What can STAR-Fusion do ?
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?
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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.
I am asking because I dont get the difference between the normal splicing indentification by STAR and the junction reads mapping by STAR-fusion.
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.
That would be nice indeed. Thanks.