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Old 01-24-2011, 11:48 PM   #1
bogdan
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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,

bogdan
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Old 01-25-2011, 12:11 AM   #2
NicoBxl
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You can use R with the package ShortRead to manipulate the reads. Bioconductor contains a lot of package to analyze HTS data. http://www.bioconductor.org/
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Old 01-25-2011, 02:46 AM   #3
A Oshlack
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This guide might be useful to you for differential expression analysis

http://seqanswers.com/forums/showthread.php?t=7068
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