Question: Estimate alternative splicing rate using RNA-Seq
gravatar for Nicolas Rosewick
5.8 years ago by
Belgium, Brussels
Nicolas Rosewick9.0k wrote:


I'm working on tumor sample (~20 samples), where three of them has a specific mutation in a gene involved in alternative splicing. We have RNA-Seq (stranded paired-end) for each of these tumors. What I want is to test if in these 3 mutated samples overall alternative splicing is dysregulated compared to non-mutated tumor. FYI we have also healthy samples.

My idea was to use MISO to make a simulation like this  (MUT = sample with mutation, NO_MUT : sample without mutation )

1. MISO analysis : 3 MUT vs 17 NO_MUT
2. Count how many genes are differentially alternativelly spliced = MISO.real
3. Pick randomly 3 samples from the pool ( 3 MUT + 17 NO_MUT ) : known as MUT.sim
4. The rest of the 17 samples of the pool : known as NO_MUT.sim
5. MISO analysis : 3 MUT.sim vs 17 NO_MUT.sim
6. Count how many genes are differentially alternativelly spliced = MISO.sim[i]
7. Return to 3. and do it N=10000 times
8. p-value = number of MISO.sim >= MISO.real / N

What do you think ? Maybe is it a better way. And of course I don't know the computational time for one MISO run ...


alternative splicing rna-seq • 2.4k views
ADD COMMENTlink modified 5.8 years ago by Charles Warden7.8k • written 5.8 years ago by Nicolas Rosewick9.0k
gravatar for Charles Warden
5.8 years ago by
Charles Warden7.8k
Duarte, CA
Charles Warden7.8k wrote:

I'm guessing you are doing this because MISO provides a Bayes factor rather than an FDR?

I would recommend trying MATS if you want a more traditional result table.

ADD COMMENTlink modified 10 months ago by RamRS28k • written 5.8 years ago by Charles Warden7.8k
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1567 users visited in the last hour