how to get TF binding affinity from ENCODE narrowPeak or broadPeak files?
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7.0 years ago
liu4gre ▴ 210

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:

1) does the region between chromStart and chromEnd mean the peak region (binding region)?

2) Does the signalValue mean the binding affinity?

3) Is it good to compare this value across cell lines to see the difference?

ChIP-Seq ENCODE narrowPeak transcription factor • 2.4k views
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