Question: workflow/tool for alternative splicing
gravatar for DavidP
3.6 years ago by
DavidP50 wrote:

Hi everyone,

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

rna-seq • 2.6k views
ADD COMMENTlink modified 22 months ago by kristoffer.vittingseerup3.0k • written 3.6 years ago by DavidP50
gravatar for EagleEye
3.6 years ago by
EagleEye6.6k wrote:

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



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

ADD COMMENTlink modified 3.6 years ago • written 3.6 years ago by EagleEye6.6k
gravatar for Charles Warden
3.6 years ago by
Charles Warden7.6k
Duarte, CA
Charles Warden7.6k wrote:

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

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

ADD COMMENTlink written 3.6 years ago by Charles Warden7.6k
gravatar for kristoffer.vittingseerup
22 months ago by
European Union
kristoffer.vittingseerup3.0k wrote:

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

ADD COMMENTlink written 22 months ago by kristoffer.vittingseerup3.0k
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