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Old 01-24-2011, 11:48 PM   #1
Location: san diego

Join Date: Jul 2008
Posts: 35
Default RNA-seq analysis packages

Dear all,

please would you have any strong recommendations regarding (user friendly) alignment method/ summarization/ differential expression method to use for RNA-seq data. As of now, Cufflinks and Cuffdiff apparently gave results that are yet not-so-meaningful. thanks a lot,

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Old 01-25-2011, 12:11 AM   #2
not just another member
Location: Belgium

Join Date: Aug 2010
Posts: 264

You can use R with the package ShortRead to manipulate the reads. Bioconductor contains a lot of package to analyze HTS data.
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Old 01-25-2011, 02:46 AM   #3
A Oshlack
Location: Australia

Join Date: Jun 2010
Posts: 17

This guide might be useful to you for differential expression analysis
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