Detecting all splicing events in RNA-Seq

Question

[Silentio]

Hi,

We are working on a project about splicing in spliceosomal introns in yeast and fungi. To summarize, we messed up with the spliceosome, and expected to see all pre-mRNAs get captured in the RNP complex without being spliced. We then pulled them down and performed RNA-Seq.

We want to validate our biochemical protocol by checking whether any splicing events happened in our samples ( welll, they should better not!). Can you please recommend any pipelines, preferably with fastq input?

[Manvendra Singh]

I think DEXSeq is good tool once you have mapped the reads using STAR or tophat

Answer 1

[Sam]

If I understand correctly, you are trying to see if there are any splicing happening at all. If that is the case, I think most RNA-Seq aligners will provide a file indicating whether if they require to split the reads in alignment and some might even include splice detection in their programme. From what I remember, you can use RNA Seq Unified Mapper, MapSplice2 etc. I can't remember if topHat2 and STAR also provide such output. You might want to check that.