Pipeline for trusight RNA fusion kit

Question

[sacha]

Hi,

Do you have any suggestion of pipeline I can use to detect fusion gene for clinical purpose ? I have data from Illumina trusight RNA kit.

Answer 1

[GenoMax]

Based on Illumina's recommendation here use STAR.

[sacha]

Ok. But this is the first step of the pipeline. I expect something more to detect fusion gene.
Thanks for the link, I will take a look.

[GenoMax]

There is a STAR-fusion package that should be useful.

Answer 2

[Charles Warden]

I think you may need some trial and error with gene fusion programs for a research project.

I've listed some other possibly useful programs below:

Clinker : used for visualization, but does some of it's own processing as well (at least the last time that I used the program)

JAFFA : gene fusion identification

As mentioned above, the aligners themselves can affect the fusion predictions:

Running STAR with parameters like --chimSegmentMin 12 --chimJunctionOverhangMin 12 (or writing some custom code from the splice junction files)

Running TopHat with --fusion-search. Sometimes, you may prefer parsing the raw output rather than trying to get the HTML TopHat-fusion summary.

I have not personally tested the trusight RNA kit, but these are generally possible options with a normal RNA-Seq experiment.