Any Promising Addition to Alternative Splicing Detection tools for Rna-Seq Data

Question

[Govardhan Anande]

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

[natasha.sernova]

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.

[Govardhan Anande]

Hi Natasha,

Thanks for quick answer.

[natasha.sernova]

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/

[Govardhan Anande]

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

[natasha.sernova]

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.

[Govardhan Anande]

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

[natasha.sernova]

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!

[Govardhan Anande]

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 [e-mail].

Thanks for your time and valuable comments.

Answer 1

[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

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