Tools for Alternative Splicing Events in RNA-Seq analysis

Tools for Alternative Splicing Events in RNA-Seq analysis


Hello community,

I’ve been doing a bit of a literature search on alternative splicing analysis using RNA-Seq data, there are quite a few tools that I have come across which I will list below. As well as some of these tools might be out of date, such as MISO. However, as I am still quite unfamiliar with this type of analysis, I wanted to know if there is a sort of a benchmark tool or a particular more novel tool accepted by the scientific community, for example, Star or Tophat for mapping/alignment. Here are the most recent tools and packages I have come across.

  1. Isoform-Centric: Integrate isoform expression estimation reveal changes in the proportion of each isoform within the total gene expression
    Relative abundance of isoforms

Algorithms: BASIS, CuffDiff2, and rSeqDiff, and Flow Difference Metric (FDM)

  1. Exon-Centric: An exon-based approach, look at all exons

Algorithms: DEXSeq

  1. Transcript Based: Used to test transcripts instead of exons

Algorithms: IsoformSwitchAnalyzeR

  1. Splicing Based: Looks at each splice even one at a time and see if there are systematic changes between conditions

Algorithms: rMATS & SUPPA2

and tool spliceR



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