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  • JonB
    Member
    • Jan 2010
    • 85
    #1

    Difference between Cufflinks coverage and HTSeq-count

    Hi,

    I am struggling to understand the coverage value (not fpkm) produced by cufflinks. In my case it seems to be much lower than the values produced by htseq-count. I thought the cufflinks coverage was the raw count? Anyone know the difference between this and the htseq-count output?

    Jon
    Tags: cufflinks, fpkm, htseq-count, rna-seq
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