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.
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written
by
sacha
2 answers
Based on Illumina's recommendation here use STAR.
There is a STAR-fusion package that should be useful.
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.
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