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  • RNA-Seq: tuxedo suite transcription start site identification

    Hi,

    I am using the most recent version of the tuxedo tools, particularly cufflinks and cummeRbund for RNA-Seq data analysis. I was wondering how you can extract the coordinates of all identified TSS from the cuffdiff output?
    Thank you very much,
    Best
    Michael

  • #2
    I am also trying to find TSS in my cuffdiff data


    Originally posted by zillerm View Post
    Hi,

    I am using the most recent version of the tuxedo tools, particularly cufflinks and cummeRbund for RNA-Seq data analysis. I was wondering how you can extract the coordinates of all identified TSS from the cuffdiff output?
    Thank you very much,
    Best
    Michael

    Comment


    • #3
      I'm pretty sure you will have to fish that out of the GTF file you used for differential testing in Ciffdiff.
      /* Shawn Driscoll, Gene Expression Laboratory, Pfaff
      Salk Institute for Biological Studies, La Jolla, CA, USA */

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