workflow/tool for alternative splicing

Question

[DavidP]

Hi everyone,

Can you recommend a good workflow (as well as tools) for alternative splicing?

Answer 1

[EagleEye]

The options are,

MISO (detailed documentation, I would recommend this)

A: What is best tool to call diferentially expressed isforms ?

A: How to determine alternative splicing read counts

Salmon

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

Sailfish

http://sailfish.readthedocs.io/en/master/sailfish.html

Or else I would recommend integration of two approaches like described in this article (salmon+MISO)

http://www.cell.com/molecular-cell/fulltext/S1097-2765(16)00047-2

Answer 2

[Charles Warden]

My latest favorite program is JunctionSeq (extends DEXSeq to include splice junctions, including novel junctions);

http://hartleys.github.io/JunctionSeq/

http://nar.oxfordjournals.org/content/early/2016/06/07/nar.gkw501

MATS is another good option, and it is a little more comprehensive with regards to the types of splicing events that are called:

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

Answer 3

[Kristoffer Vitting-Seerup]

I just pushed an update of my R package IsoformSwitchAnalyzeR to Bioconductor which introduces a module for alternative splicing. For individual splice sites the already suggested tools are probably better - but for a genome wide analysis of splicing it is very convenient to frame it as a comparison of isoforms that are switching since it allows for easy interpretation and statistical analysis. For examples of what it can do see the alternative splicing part of the vignette here