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Old 07-30-2010, 12:44 PM   #1
IrisZhu
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Post advanced tools in RNA-seq analysis

Hello All,

My boss asked me to use at least three most commonly used RNA-seq analysis software/tools to process some data (paired end, 75 bp, human) and compare them. I know that Tophat/Cufflinks is a very powerful and popular pipeline -- from mapping to assembly.

What else? Could anybody give me some suggestions?

Thanks!!

Iris

Last edited by IrisZhu; 07-30-2010 at 12:50 PM.
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Old 07-30-2010, 12:52 PM   #2
ECO
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Might I suggest: http://seqanswers.com/wiki/Special:BrowseData

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Old 07-30-2010, 12:57 PM   #3
Nix
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Check out http://useq.sourceforge.net/ and the user guide describing differential transcriptome analysis http://useq.sourceforge.net/usage.html .
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Old 08-02-2010, 07:38 AM   #4
IrisZhu
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Very helpful!
Thank you guys.
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Old 08-03-2010, 12:19 AM   #5
Gangcai
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You can try scripture for assembly also : http://www.broadinstitute.org/software/scripture/
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Old 08-05-2010, 12:34 PM   #6
IrisZhu
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Quote:
Originally Posted by Gangcai View Post
You can try scripture for assembly also : http://www.broadinstitute.org/software/scripture/
Thanks! Have you ever used it? Seems it requires some pre-processing of Tophat output files.
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Old 08-05-2010, 04:57 PM   #7
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I am trying to use scripture now. Yes , it needs some pre-processing of tophat output files, including combining, sorting, and indexing. I have just finished the pre-processing right now.
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