I just learn to understanding ENCODE ChiP-Seq data for Transcription Factor binding. I looked at the narrowpeak files and find there is a column named "Score". Is this the tag density indicating the binding affinity of TF at this site or region? If not, how can I get the tag density (or binding affinity)?
Question: NarrowPeak format of ChiP-seq
6.0 years ago by
liu4gre • 200
liu4gre • 200 wrote:
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6.0 years ago by
Sukhdeep Singh ♦ 10k
Sukhdeep Singh ♦ 10k wrote:
ENCODE narrowPeak: Narrow (or Point-Source) Peaks format
This format is used to provide called peaks of signal enrichment based on pooled, normalized (interpreted) data. It is a BED6+4 format.
- chrom - Name of the chromosome (or contig, scaffold, etc.).
- chromStart - The starting position of the feature in the chromosome or scaffold. The first base in a chromosome is numbered 0.
- chromEnd - The ending position of the feature in the chromosome or scaffold. The chromEnd base is not included in the display of the feature. For example, the first 100 bases of a chromosome are defined aschromStart=0, chromEnd=100, and span the bases numbered 0-99.
- name - Name given to a region (preferably unique). Use '.' if no name is assigned.
- score - Indicates how dark the peak will be displayed in the browser (0-1000). If all scores were '0' when the data were submitted to the DCC, the DCC assigned scores 1-1000 based on signal value. Ideally the average signalValue per base spread is between 100-1000.
- strand - +/- to denote strand or orientation (whenever applicable). Use '.' if no orientation is assigned.
- signalValue - Measurement of overall (usually, average) enrichment for the region.
- pValue - Measurement of statistical significance (-log10). Use -1 if no pValue is assigned.
- qValue - Measurement of statistical significance using false discovery rate (-log10). Use -1 if no qValue is assigned.
- peak - Point-source called for this peak; 0-based offset from chromStart. Use -1 if no point-source called.
Here is an example of narrowPeak format:
track type=narrowPeak visibility=3 db=hg19 name="nPk" description="ENCODE narrowPeak Example" browser position chr1:9356000-9365000 chr1 9356548 9356648 . 0 . 182 5.0945 -1 50 chr1 9358722 9358822 . 0 . 91 4.6052 -1 40 chr1 9361082 9361182 . 0 . 182 9.2103 -1 75
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