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 As well as some of these tools might be out of date, such as MISO.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.
- 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)
- Exon-Centric: An exon-based approach, look at all exons
Algorithms: DEXSeq
- Transcript Based: Used to test transcripts instead of exons
Algorithms: IsoformSwitchAnalyzeR
- 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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