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  • rainmaker
    Junior Member
    • Jul 2013
    • 1
    #1

    Referance Genome - Noob Question

    Hello eveyone,

    I'm very new at this subject, and I need help about alingment of RNA-seq reeds. I want to make some trys on the data(>110GB) of this project. I downloaded Sequence Read Archive (SRA) from NCBI. How can I make an alignment on them. How can I use TopHat without refererance genome or how can I find reference genome of all primates which is used in this project.

    Or am I thinking very wrong by thinking to make DEseq on primates RNAseq data.

    If you know a tutorial page or video for this job please share with me.

    Please don't hurt me about my noob question, you can share with me other basic question forums.

    Thank you...
    Last edited by rainmaker; 07-06-2013, 07:10 AM.
    Tags: deseq, reference genome, rnaseq
    • mastal
      Senior Member
      • Mar 2009
      • 666
      #2
      Referance Genome - Noob Question

      The paper you mentioned has links to the software that they used for the analysis.

      You could try downloading and trying that software, or you could use the Trinity software, from the Broad Institute

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