Tools for Alternative Splicing Events in RNA-Seq analysis

Question

[joe_genome]

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 As well as some of these tools might be out of date, such as MISO.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

[ATpoint]

For anything that relates to isoform quantifications you should read up on lightweight pseudo/selective aligners such as salmon which can produce inferential replicates and then tools which build on this, e.g. the swish method which then incorporates these mapping uncertanties into the testing precedure.

https://salmon.readthedocs.io/en/latest/salmon.html

https://bioconductor.org/packages/release/bioc/vignettes/fishpond/inst/doc/swish.html