Question: workflow/tool for alternative splicing
3
gravatar for DavidP
2.9 years ago by
DavidP50
DavidP50 wrote:

Hi everyone,

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

rna-seq • 2.2k views
ADD COMMENTlink modified 14 months ago by kristoffer.vittingseerup1.8k • written 2.9 years ago by DavidP50
3
gravatar for EagleEye
2.9 years ago by
EagleEye6.4k
Sweden
EagleEye6.4k 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

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

ADD COMMENTlink modified 2.9 years ago • written 2.9 years ago by EagleEye6.4k
1
gravatar for Charles Warden
2.9 years ago by
Charles Warden6.9k
Duarte, CA
Charles Warden6.9k wrote:

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/

ADD COMMENTlink written 2.9 years ago by Charles Warden6.9k
0
gravatar for kristoffer.vittingseerup
14 months ago by
European Union
kristoffer.vittingseerup1.8k 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 14 months ago by kristoffer.vittingseerup1.8k
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