Question: how to get TF binding affinity from ENCODE narrowPeak or broadPeak files?
0
gravatar for liu4gre
5.5 years ago by
liu4gre200
United States
liu4gre200 wrote:

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 • 2.2k views
ADD COMMENTlink modified 5.4 years ago by biostart340 • written 5.5 years ago by liu4gre200
3
gravatar for biostart
5.4 years ago by
biostart340
Germany
biostart340 wrote:

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

ADD COMMENTlink written 5.4 years ago by biostart340
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