Question: Calling Exon Skipping Events from RNA-Seq
0
gravatar for mrxcm3
5 days ago by
mrxcm340
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?

Thanks

rna-seq star fusion • 81 views
ADD COMMENTlink modified 3 days ago by gianluca.dellavedova50 • written 5 days ago by mrxcm340
1

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
1

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
0
gravatar for gianluca.dellavedova
3 days ago by
Italy
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
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1436 users visited in the last hour