What is point source in the narrow peak format

Question

[msharmin]

Hi all,

The last column of the narrow peak format of Chip-Seq data is called point source. What is the purpose of this column? Couple of friends told me it might mean the tip of the peak. However, when I looked at the data I found point source often falls outside the narrow peak region itself. I am giving an example below...

> head(tfbs)
    chr     start       end name score strand    value  p        q point
1  chr3 119187486 119188061    .  1000      . 437.4133 -1 4.184663   283
2  chr9 115818601 115819287    .  1000      . 437.3500 -1 4.184663   417
3 chr19  37663509  37664035    .  1000      . 426.5352 -1 4.184663   264
4  chr1 161195562 161196244    .  1000      . 423.0543 -1 4.184663   280
5  chr7 102789692 102790388    .  1000      . 414.2319 -1 4.184663   373
6 chr12  72057639  72058324    .  1000      . 407.5873 -1 4.184663   388

> sum((tfbs$end-tfbs$start)>tfbs$point)
[1] 10255

Thanks in advance for help.

[Devon Ryan]

While it's supposed to be the 0-based offset from column 2 of the peak, that's apparently not being adhered to in the dataset you're looking at. Where did you get the file?

[msharmin]

It's directly downloaded from encode experimental matrix. Following is detail info...this is just an example...other narrow peak files give me the same concern.

A549 (EtOH .02) TFBS Uniform Peaks of YY1_(SC-281) ENCODE/HudsonAlpha/Analysis

shortLabel:                            A549+Et.02 YY1
Lab producing data:                    Myers - Hudson Alpha
Experiment (Assay) type:               ChIP-seq
View - Peaks or Signals:               Peaks
Cell, tissue or DNA sample:            A549
Antibody target:                       YY1
Treatment:                             EtOH 0.02% 1h
Antibody or target protein:            YY1 (sc-281)
ENCODE Data Freeze:                    ENCODE Mar 2012 Freeze
UCSC Accession:                        wgEncodeEH002282
ControlId - explicit relationship:     SL6021
Integrated quality flag:               Good
tableName:                             wgEncodeAwgTfbsHaibA549Yy1cV0422111Etoh02UniPk
fileName:                              wgEncodeAwgTfbsHaibA549Yy1cV0422111Etoh02UniPk.narrowPeak.gz

File URL: http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsHaibA549Yy1cV0422111Etoh02UniPk.narrowPeak.gz