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Old 04-20-2016, 05:48 AM   #1
Location: Germany

Join Date: Dec 2013
Posts: 16
Default 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,
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