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  • schaffer
    Member
    • Apr 2009
    • 12
    #1

    Compare RNA counts: HTSeq vs Partek

    Simon,
    I have mapped reads with TopHat and then compared the exon counts from both HTseq and Partek method. There are 2x mapped reads found with Partek compared to HTseq-count. Some of the mRNAs show about the same number of counts for both methods. However, most show big differences.

    Partek HTSeq-both strands
    gene title cDNA+ cDNA- Column 1 cDNA+ cDNA-
    MUC16 11 263 MUC16 14 299
    DIFFERENT:
    RHOU 89 714.678 RHOU 0 23
    MUC12 20 283 MUC12 4 73
    TTN 6.95E-05 268.507 TTN 9 464

    Can you suggest how to a way to know why they differ?
    Thanks,
    Lana
    Tags: None
    • Simon Anders
      Senior Member
      • Feb 2010
      • 995
      #2
      What do "cDNA+" and "cDNA-" mean?

        Comment

        • schaffer
          Member
          • Apr 2009
          • 12
          #3
          different sample conditions

          Simon,
          These are sample conditions and not sample replicates.
          Lana

            Comment

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