RNAseq Alternative Splicing

[awk]

I'm looking for accuracy tool to identify alternative splicing in RNAseq reads.

Best,

[cedance]

Tophat is one popular software that is capable of aligning spliced reads. It gives you a BAM output file. You should read SAM format manual to understand this format. Then it gets pretty straightforward to identify AS events by yourself.

If you want to quantify isoform/transcript abundance, you could use Cufflinks (after using tophat).

Hope this helps.

[awk]

Dear cedance,

Thank for your advice. I used Tophat and also Cufflinks however I´m looking for alternative software.

For instance I read that other possibility are MapSplice and AStalavista. As you know many tools exist but my priority is the accuracy in alternative splicing detection.

Best,

[areyes]

Give a try to DEXSeq!

http://watson.nci.nih.gov/bioc_mirror/packages/2.9/bioc/html/DEXSeq.html

[awk]

DEXSeq

Dear areyes,

I read DeXSeq description and I really interested in used it for exon differential expression analysis.

However the DEXSeq library is available only in R version 2.14.0 (unstable and not available for linux).

I would like to know if a DEXSeq version is also for R version 2.13.0.

Best,

[areyes]

Hi,

Indeed, DEXSeq is in the development branch of Bioconductor and available in R version 2.14. But you can of course find the sources for this version for linux in the R cran webpage:

http://cran.r-project.org/

If you really want to use R-2.13 you can also download DEXSeq manually and install it from the command line.

[awk]

Thanks areyes for you advice.

I will try to do.

[steven]

Dear cedance,

Thank for your advice. I used Tophat and also Cufflinks however I´m looking for alternative software.

For instance I read that other possibility are MapSplice and AStalavista. As you know many tools exist but my priority is the accuracy in alternative splicing detection.

Best,

Hi,
Out of curiosity, why aren't you satisfied with TopHat/Cufflinks?
If I remember correctly Astalavista is dedicated to the detection of all possible alternative splicing events (exon skipping, etc) from a set of annotated transcripts.
The Flux Capacitor may be an option.
cheers,
s.

[awk]

Dear steven,

I apologize for the misunderstanding. What I wanted to say is that I´m interested in testing different approaches and not that I´m not satisfied with TopHat/Cufflinks.

I will considered also Flux Capacitor.

Thanks for your advice.

[steven]

No problem, I was just curious -I am not involved in Cufflinks, but interested in any opinion. As for the Flux, its author may work in your building (or used to). Say hi from steven if you talk to him

[songyj]

SOAPsplice

Give a try to DEXSeq!

http://watson.nci.nih.gov/bioc_mirro...ml/DEXSeq.html

what about SOAPsplice?
Introduction
SOAPsplice: We have developed a tool SOAPsplice for genome-wide ab initio detection of splice junction sites from RNA-Seq, a method using new generation sequencing technologies to sequence the messenger RNA.

http://soap.genomics.org.cn/soapsplice.html

[cedance]

Dear cedance,
Thank for your advice. I used Tophat and also Cufflinks however I´m looking for alternative software.

For instance I read that other possibility are MapSplice and AStalavista. As you know many tools exist but my priority is the accuracy in alternative splicing detection.
Best,

What is your criteria for deciding which of the softwares are the most accurate in splice site detection?

[Simon Anders]

To clarify: Most of the tools mentioned above help you in discovering and/or quantifying alternative isoform usage, i.e., to see which isoforms are present in a given sample. If you have samples from two different experimental conditions, you may want to compare and find genes for which the isoform abundance ratios are influenced by the treatment. DEXSeq is meant for the latter.

[cedance]

Simon, thanks for the clarification. Could you briefly explain (or point to a link) regarding the reason/usage of <negative binomial distribution> for variance estimation over two biological replicates? Also, why wouldn't this package be useful, say, if I want to compare differential exon expression between two species?

[steven]

To clarify: Most of the tools mentioned above help you in discovering and/or quantifying alternative isoform usage, i.e., to see which isoforms are present in a given sample. If you have samples from two different experimental conditions, you may want to compare and find genes for which the isoform abundance ratios are influenced by the treatment. DEXSeq is meant for the latter.

Thank you Simon. I think that Cufflinks also provides a statistical test to check if the relative contribution of each isoform is significantly different between two biological groups.