Question: Any Promising Addition to Alternative Splicing Detection tools for Rna-Seq Data
1
gravatar for Govardhan Anande
3.5 years ago by
Australia
Govardhan Anande130 wrote:

Hello,

I know bunch of tools for Alternative Splicing Detection and quantification From Rna-Seq Data like MISO, DEXseq, MATS, SpliceR etc.

Please suggest any new promising tool/tools rather than MISO, DEXseq, MATS & SpliceR. If anyone can advise any review article regarding comparison of all tools used for alternative splicing analysis then that will be helpful too.

Thanks,

Govardhan

sequencing rna-seq next-gen • 2.2k views
ADD COMMENTlink modified 18 months ago by kristoffer.vittingseerup2.4k • written 3.5 years ago by Govardhan Anande130

Splicing:

Some biostar posts:

Recommended Tools For Alternative Splicing Detection From Rna-Seq Data

Splicing detection software, recent reviews:

http://www.hindawi.com/journals/bmri/2015/831352/

in humans:

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3903050/

in plants:

http://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-014-0364-4

a relatively new method, SplicingCompass (2013)

http://bioinformatics.oxfordjournals.org/content/early/2013/03/22/bioinformatics.btt101.long

Methods to study splicing from high-throughput RNA Sequencing data

https://arxiv.org/ftp/arxiv/papers/1304/1304.5952.pdf

Hopefully, there is some useful information for you here.

ADD REPLYlink modified 3.5 years ago • written 3.5 years ago by natasha.sernova3.6k

Hi Natasha,

Thanks for quick answer.

ADD REPLYlink written 3.5 years ago by Govardhan Anande130

Hello, Govardhan!

Unfortunately you did not tell us what organisms you are working with,

if you are a theoretician or experimental biologist, etc.

There are hundreds of nice papers describing alternative splicing detection tools but without these

information it’s very hard to find something useful for you.

There are some other articles below but I have not known what exactly to search for.

SROOGLE: webserver for integrative, user-friendly visualization of splicing signals

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2703896/

Experimental Assessment of Splicing Variants Using Expression Minigenes and Comparison with In Silico Predictions

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4425124/

Exon First Nucleotide Mutations in Splicing: Evaluation of In Silico Prediction Tools

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3931810/

ADD REPLYlink modified 3.5 years ago • written 3.5 years ago by natasha.sernova3.6k

Hi Natasha,

I am bioinformatician, and I am working on Human. I worked on few tools like MISO, DEXseq, Cufflinks etc but unformtunatly every tool behaves differently for same data. So here "BIOSTAR" I am trying to get opinion on the best one to consider.

Hopefully, this info will be sufficient and if you need further info let me know.

Thanks, Govardhan

ADD REPLYlink written 3.5 years ago by Govardhan Anande130

Thank you, Govardhan, it's enought, I know about this problem from a different area. So what I did. I've selected a clear user-friedly program, published in good journals many times and I've used it since then. I've met its authors and I respect these people. I discuss some updates of the program with them regularly, they are very helpful people. These are my criteria.

ADD REPLYlink written 3.5 years ago by natasha.sernova3.6k

So what will be your final suggestion for me ???? Any final candidate(tool) u would like to recommend ???

ADD REPLYlink written 3.5 years ago by Govardhan Anande130

The name I know as a synonim of splicing is Gil Ast.

His server SROOGLE I've mentioned. It may be not exacly what you wanted...

Look at the papers citing his article as well, some tools are mentioned there.

Good luck!

ADD REPLYlink modified 3.5 years ago • written 3.5 years ago by natasha.sernova3.6k

I will have a look. If you don't mind can you provide me your email/Skype ID to have discussion in future, my email ID is govardhananade@gmail.com.

Thanks for your time and valuable comments.

ADD REPLYlink written 3.5 years ago by Govardhan Anande130
1
gravatar for kristoffer.vittingseerup
18 months ago by
European Union
kristoffer.vittingseerup2.4k 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

As a bonus IsoformSwitchAnalyzeR also allows you to identify and analyze isoform switches with predicted functional consequences

ADD COMMENTlink written 18 months ago by kristoffer.vittingseerup2.4k
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