Calling Exon Skipping Events from RNA-Seq

Question

[mrxcm3]

I have RNA-Seq data from tumour samples and references, and I have had success calling gene fusion events. However, although I have tried a range of fusion detection tools, none of them are able to detect within-gene ('exon skipping') events such as MET ex14 skipping or EGFR vIII. I have also tried some SV callers like MANTA without any luck.

I do not want to perform differential expression / exon usage - this is just an detection exercise. Is anyone able to suggest any tools that detect exon skipping events from RNA-seq data please?

Thanks

[lieven.sterck]

in this paper they developed a tool called findAS, not sure if applicable for your situation.

more in general, I suggest to have a look at (google for) alternative splicing detection tools

[mrxcm3]

thanks lieven.sterck. I will take a look for sure.

[igor]

Some relevant previous discussions:

• Tools To Do the Alternative Splicing Analysis
• differential exon usage
• exon skipping and RNA-Seq

Answer 1

[gianluca.dellavedova]

We have developed ASGAL for that purpose, and we are still maintaining and extending it. Feel free to open an issue if you need help.