What does average signal enrichment of a region in Chip-seq peak file means?

Question

[atsalaki]

Score denotes average signal enrichment for the region. This is written in chip-seq peak files bed format in ENCODE. Can someone explain to me what this means?

Answer 1

[Carlo Yague]

This is the average (between replicates) read count over the region. If the score is high, it means that a lot of chromatin from that region is pulled down by the IP and sequenced.

Of course, the full analytical method is more complicated than that with filtering, normalization, peak calling, ... If you need more details I suggest you read the ENCODE paper such as this one.