Pipeline for trusight RNA fusion kit
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6.1 years ago
sacha ★ 2.4k

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.

RNA-Seq • 1.3k views
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6.1 years ago
GenoMax 146k

Based on Illumina's recommendation here use STAR.

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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.

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

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6.1 years ago

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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