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  • Cuffdiff and graphics

    Hi everybody
    Now that I could get (painfully ;-)) through the whole analysis of our RNA-seq data using Galaxy, I am quite puzzled on how produced some decent and informative graphic information (exonic vs. intronic hits; number of novel transcripts, differential splicing events etc) starting from this tab files roduced by Cufflinks/Cuffdiff...
    Any (simple) hints for somebody working under a Win 7 environment (yes I am not a computer wiz, just a biologist diving into digital biology )??
    Thanks!

  • #2
    Hi,

    we (Genomatix) have released a new tool called Transcriptome Viewer, with the goal to visualize RNA-seq mapping to transcripts, exons and splice-junctions in light of the annotated transcriptome (see attached screenshots). This tool, however, is not based on Tophat/Cufflinks mapping but on our own mapping and RNA-seq approach.

    The reason we did this was that we saw the same problem you are pointing out: a lack in visualization tools for RNA-seq workflows. Currently, RNA-seq results are mostly visualized in genome browsers but not in dedicated RNA-seq visualization tools.

    Regards
    Attached Files

    Comment


    • #3
      Thanks, I guess you are referring to the "mygenomatix" software suite?

      Comment


      • #4
        Right, the Transcriptome Viewer is part of mygenomatix.com.

        Comment


        • #5
          There are command line tools that you can use to do the things you want, but a fairly simple alternative would be to try out SeqMonk for producing some graphics.

          There are even some helpful demo videos on Youtube.

          Comment


          • #6
            Seq monk

            How the analysis is done should not matter where one is doing visulaization I mean they may or may not match??

            Comment

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