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  • Relative STrand Cross-correlation coefficient (RSC) negative value???

    Hi All,

    I am trying to obtain the RSC value using Phantompeakqualtool on my single-end 50bp ChIP-seq data. No replicate. However, I realize that I am getting a very strange RSC value. It is negative?

    Code:
    Reading Control tagAlign/BAM file TAC_input.bam 
    opened /tmp/RtmpKXlVct/TAC_input.tagAlign16bc12361f946
    done. read 1572027 fragments
    Control data read length 50 
    Calculating peak characteristics
    Minimum cross-correlation value 0.06543415 
    Minimum cross-correlation shift 1500 
    Top 3 cross-correlation values 0.173582627089614 
    Top 3 estimates for fragment length 0 
    Window half size 0 
    Phantom peak location 50 
    Phantom peak Correlation 0.06434206 
    Normalized Strand cross-correlation coefficient (NSC) 2.652784 
    Relative Strand cross-correlation Coefficient (RSC) -99.02962 
    Phantom Peak Quality Tag NA

    My question is how do I intepret this negative value? Can I treat it as 0 since the minimum number of RSC is 0?

    Thank you.

    Wilson

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