effect of Non coding RNA in alternative splicing changes

Question

[elhamdallalbashi]

Hi all, How can I find the effect of Non coding RNA in alternative splicing changes in two case of control/treatment? actually I work on Non coding, But small part of my thesis is related to effect of Non coding RNA in alternative splicing,for this reason I need a simple way.

[WouterDeCoster]

What type of data do you have?

[elhamdallalbashi]

I have RNA-seq data.

[WouterDeCoster]

What's the hypothesis? How would non-coding RNA in your opinion have an effect on splicing? Are you talking about miRNAs? lncRNAs? UTRs? Is there a reason to expect that in your comparison between control and "treatment" there woud be a difference in the splicing due to non-coding RNAs? I don't really understand the rationale of the experiment.

[elhamdallalbashi]

I work on miRNAs and lncRNAs. let me explain, I work on RNAseq data (effect of drug on cancer), I want to study difference in efficacy of non coding in splicing, before and after treatment.is not true or possible?

[WouterDeCoster]

difference in efficacy of non coding in splicing

This is doesn't make sense to me, can you explain?

[elhamdallalbashi]

A variety of long and short non-coding RNAs mediate regulation of gene expression at multiple levels (e.g. splicing). in other hand it is clear that in absence or present of drug, regulation of non-coding change.now I want to study effect of non-coding differential expression in alternative splicing. I hope you understand what I mean؟

[WouterDeCoster]

You can investigate whether between treatment and control there is alternative splicing in your dataset, but you cannot determine if that is caused by non-coding RNAs (you can not conclude such a causal relationship).

[elhamdallalbashi]

OK, please tell me how can I investigate whether between treatment and control there is alternative splicing in my dataset?

[WouterDeCoster]

I would suggest to have a look in the following thread: Recommended Tools For Alternative Splicing Detection From Rna-Seq Data

[Farbod]

Hi, what kind of animal you are working with?

[elhamdallalbashi]

Hi Farbod,I work on human RNAseq data

[Farbod]

Dear WouterDeCoster and Elham Hi,

Is it some kind of research that will focus on the number of isoforms each transcripts would have in the present or absent of a set of Non coding RNAs?

~ Best

[elhamdallalbashi]

I think they are same,is it possible to explain what you are doing?