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Old 01-24-2010, 08:59 PM   #1
jiwu2573
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Question Alternative splicing detection using RNA-seq

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.
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Old 01-26-2010, 03:11 AM   #2
Cole Trapnell
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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.
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Old 01-26-2010, 02:25 PM   #3
jiwu2573
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Thanks!

I think many working with RNA sequencing are looking forward to the release!
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Old 01-26-2010, 02:28 PM   #4
shurjo
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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
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Old 01-28-2010, 03:19 AM   #5
GoneSouth
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Default great news

Yeesss!
Happy to hear this!
Thanks for the great tool!
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Old 01-28-2010, 06:05 AM   #6
Nix
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Default 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
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Old 01-28-2010, 08:20 AM   #7
Cole Trapnell
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Quote:
Originally Posted by shurjo View Post
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.
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Old 01-28-2010, 01:57 PM   #8
mgogol
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Default Congratulations!

And thanks for all your hard work.
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Old 01-28-2010, 10:20 PM   #9
shurjo
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Welcome to the married men's club, Cole. I'll wait even more patiently for cuffdiff now that I know you're married too.
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Old 02-05-2010, 08:56 PM   #10
shurjo
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It's out! I will try it this weekend and post feedback.
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