how to get TF binding affinity from ENCODE narrowPeak or broadPeak files?
I just learn to understanding ENCODE ChiP-Seq data for Transcription Factor binding. I know the narrowPeak format consists BED6+4 columns which is described in https://genome.ucsc.edu/FAQ/FAQformat.html#format12. My question is:
- Does the region between chromStart and chromEnd mean the peak region (binding region)?
- Does the signalValue mean the binding affinity?
- Is it good to compare this value across cell lines to see the difference?
1 answer
1) yes, it's the peak region, but it might be significantly larger than the individual TF binding site
2) This value gives the ChIP-seq peak strength. It is usually correlated with the binding affinity, but not necessarily.
3) no, the ChIP-seq enrichments in different experiments can differ for non-biological reasons
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