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
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.
Hi Natasha,
Thanks for quick answer.
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/
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
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.
So what will be your final suggestion for me ???? Any final candidate(tool) u would like to recommend ???
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!
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.