Question: Methods or packages for identifying differential splicing
1
gravatar for Daniel Standage
4.8 years ago by
Daniel Standage3.8k
Davis, California, USA
Daniel Standage3.8k wrote:

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?

rna-seq alternative-splicing • 2.1k views
ADD COMMENTlink modified 20 months ago by kristoffer.vittingseerup1.4k • written 4.8 years ago by Daniel Standage3.8k

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

ADD REPLYlink written 4.4 years ago by Manvendra Singh2.0k
2
gravatar for Charles Warden
4.8 years ago by
Charles Warden6.1k
Duarte, CA
Charles Warden6.1k wrote:

MATS is my favorite tool for splicing event prediction:

http://rnaseq-mats.sourceforge.net/

MISO is another popular option:

http://genes.mit.edu/burgelab/miso/

ADD COMMENTlink modified 4.8 years ago • written 4.8 years ago by Charles Warden6.1k

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.

ADD REPLYlink written 2.9 years ago by eduardo.eyras0
2
gravatar for kristoffer.vittingseerup
20 months ago by
European Union
kristoffer.vittingseerup1.4k wrote:

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

ADD COMMENTlink written 20 months ago by kristoffer.vittingseerup1.4k
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