exon skipping and RNA-Seq

Question

[qudrat]

Hello all, I have downloaded a BAM file and I want to study exon skipping of all the genes whether novel or known. Is there any software available for the same purpose?

Answer 1

[Devon Ryan]

Have a look at the rMATS package, which can be used for this.

Answer 2

[twrzes]

Hi,

I would suggest using LeafCutter:

http://davidaknowles.github.io/leafcutter/

https://www.biorxiv.org/content/early/2017/09/07/044107

Cheers, T

Answer 3

[Omics data mining]

Dear Devon,

I have multiple samples to analysis alternative splicing in normal vs tumour samples. Due to system compatibility and memory issues, I am not able to run rMATS . Is there any other reliable Tool which could take the reads count as input and provide output just like rMATS which is more interpretable and easy to understand. Could you suggest me other way to analyse alternative splicing.

Thank you in advance

[Kristoffer Vitting-Seerup]

Did you try rMATS v4.0.1 or higher? (They made some large updates there).

Answer 4

[Kristoffer Vitting-Seerup]

If you are more interested in isoform switches - where you can acutally start predicting the consequences - you should take a look at my tool IsoformSwitchAnalyzeR which can help you identification and analysis of isoform switches with predicted functional consequences (such as gain/loss of protein domains etc) and includes features for visualizing both single and global events.