I am wondering if it is OK to use signal value stored in narrowPeak format (ENCODE) to represent the binding affinity of a specific TF?
If yes, is this value comparable across samples?
Is it same to tag density?
If not, how can I calculate the binding affinity from narrowPeak file or bam file?
Thanks.
1 answer
signal.value from narrowPeak is from SPP peak caller
This value is not comparable across samples
It is related to tag density
You can count read overlapping the peaks, see this
Be sure to normalize after you count your reads (peaks have diff sizes and different samples will have different read depths)
See this for more information on what does signal.value mean for ENCODE narrowPeak files: https://sites.google.com/site/anshulkundaje/projects/idr
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