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RNA-seq analysis packages

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  • 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

  • #2
    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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    • #3
      This guide might be useful to you for differential expression analysis

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

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