Methods or packages for identifying differential splicing

Question

[Daniel Standage]

I have 12 RNA-Seq samples corresponding to 6 biological replicates each of 2 conditions. Is there an overview of methods for identifying differential splicing from RNA-Seq data? By differential splicing, I don't mean alternative splicing in general, but specific cases in which Condition A uses a particular isoform of a gene and Condition B uses a different isoform of that gene.

I'm aware that Cufflinks (Cuffdiff specifically) performs differential splicing tests. Are there any other documented tools or methods for doing this?

[Manvendra Singh]

I think DEX-Seq package is very powerful for your reason

Answer 1

[Charles Warden]

MATS is my favorite tool for splicing event prediction.

MISO is another popular option.

[eduardo.eyras]

Hi,

rMATS now allows to use multiple replicates per condition. MISO does not allow replicates and DEXSeq won't give you a clear description of alternative splicing events. Similarly, Cuffdiff tells you that the gene has some differential splicing but it is not clear what is changing. rMATs is better for that. We're now adding diff. splicing analysis to SUPPA using multiple replicates per condition. Hopefully it will be ready soon. cheers E.

Answer 2

[Kristoffer Vitting-Seerup]

I know the question is quite old but I'd like to add an answer for future reference.

If you are interested in isoform switches (as opposed to differential exon analysis) a potential tool could be IsoformSwitchAnalyzeR ( https://bioconductor.org/packages/devel/bioc/html/IsoformSwitchAnalyzeR.html ) which directly parses cufflinks/cuffdiff output (although other tools such as Kallisto/Salmon/RSEM are also supported) and enables identification of isoform switches with predicted functional consequences where the consequences can be chosen from a long list but includes protein domains etc

Hope this helps Kristoffer