Question: Calling Exon Skipping Events from RNA-Seq
gravatar for mrxcm3
5 days ago by
mrxcm340 wrote:

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?


rna-seq star fusion • 81 views
ADD COMMENTlink modified 3 days ago by gianluca.dellavedova50 • written 5 days ago by mrxcm340

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

ADD REPLYlink modified 5 days ago • written 5 days ago by lieven.sterck7.8k

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

ADD REPLYlink written 5 days ago by mrxcm340

Some relevant previous discussions:

ADD REPLYlink written 4 days ago by igor10k
gravatar for gianluca.dellavedova
3 days ago by
gianluca.dellavedova50 wrote:

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.

ADD COMMENTlink written 3 days ago by gianluca.dellavedova50
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