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Quantifying ChIPseq signal for one sample

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  • Quantifying ChIPseq signal for one sample

    Hey Everybody,

    I am trying to rank genes according to their phosphorylated CTD Pol II occupancy as a rough estimate of ongoing transcription.

    I am using ENCODE Pol2 ChIPseq data, which means I have access to called peaks, raw and wiggle files. I would like to ask you if it's generally a good strategy to quantify signal from bigWig file using bigWigAverageOverBed UCSC tool for all the human genes in given cell line. I avoided using called narrow peaks in this case, as I believe this would approximate the polymerase stalling better than the actual transcription.

    To assess this approach, I am correlating this quantified signal to RNAseq RPKM values from the same cell line and get Spearman correlation coefficient of around 0.62.

    Is there a better way to rank genes by their ChIPseq signal in a single sample?

    Thanks for any suggestions,

  • #2
    Something along those lines should work. We normally use computeMatrix from deepTools for this sort of purpose, but if you only want a single value then bigWigAverageOverBed should give equivalent results.


    • #3
      As always very helpful, Devon, I owe you few beers already

      Thanks for the tip!