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  • Gangcai
    replied
    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.

    Leave a comment:


  • IrisZhu
    replied
    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.

    Leave a comment:


  • Gangcai
    replied
    You can try scripture for assembly also : http://www.broadinstitute.org/software/scripture/

    Leave a comment:


  • IrisZhu
    replied
    Very helpful!
    Thank you guys.

    Leave a comment:


  • Nix
    replied
    Check out http://useq.sourceforge.net/ and the user guide describing differential transcriptome analysis http://useq.sourceforge.net/usage.html .

    Leave a comment:


  • ECO
    replied
    Might I suggest: http://seqanswers.com/wiki/Special:BrowseData

    Leave a comment:


  • IrisZhu
    started a topic advanced tools in RNA-seq analysis

    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, 12:50 PM.

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