Alternative splicing detection using RNA-seq

[jiwu2573]

I used Bowtie and Tophat to align my reads and to identify splice junctions but now i would like to be able to compare my two conditions.

I am looking for something that uses mRNA-seq to identify novel splicing events in a given sample or, if multiple samples are available, identifies differential splicing events between those samples.

Has anyone come across some software that can do these things?

Thanks in advance.

[Cole Trapnell]

The next release of Cufflinks (planned for next week) will include a new tool, cuffdiff, that will perform a comprehensive battery of differential expression and differential splicing tests on two or more samples. I will post a detailed message to the forums detailing the new tool and announcing its release.

[jiwu2573]

Thanks!

I think many working with RNA sequencing are looking forward to the release!

[shurjo]

Can't wait! Can I be horribly greedy and ask if the release is happening toward the beginning or ending of next week?

Thanks,

Shurjo

[GoneSouth]

great news

Yeesss!
Happy to hear this!
Thanks for the great tool!

[Nix]

USeq does differential RNA-Seq

Check out the USeq package. http://useq.sourceforge.net

I've added functionality to look for changes in expression and structure for known genes (no novel discovery) using binomial and chi-square tests respectively.

There's a detailed tutorial too http://useq.sourceforge.net/usage.html

[Cole Trapnell]

Can't wait! Can I be horribly greedy and ask if the release is happening toward the beginning or ending of next week?

Thanks,

Shurjo

I can't make any promises, but I'll try to get it out earlier rather than later. I have a mountain of email to respond to from being away from machines for 3 weeks (honeymoon), and I don't want to try our users' patience anymore than I already have.

[mgogol]

Congratulations!

And thanks for all your hard work.

[shurjo]

Welcome to the married men's club, Cole. I'll wait even more patiently for cuffdiff now that I know you're married too.

[shurjo]

It's out! I will try it this weekend and post feedback.