Question: how is obtained the BED score values (the 5th column of the bed files) in BED files
0
gravatar for fusion.slope
2.2 years ago by
fusion.slope200
fusion.slope200 wrote:

Hello,

am wondering if anyone of you know how is obtained the BED score values (the 5th column of the bed files) of BED files. In UCSC is written:

"score - A score between 0 and 1000. If the track line useScore attribute is set to 1 for this annotation data set, the score value will determine the level of gray in which this feature is displayed (higher numbers = darker gray). This table shows the Genome Browser's translation of BED score values into shades of gray.."

But how is it obtained?

Thanks in advance for any help.

bed files chip-seq score • 2.0k views
ADD COMMENTlink modified 18 months ago by augustin.le_bouquin0 • written 2.2 years ago by fusion.slope200

Typically, the score is usually stored in the fifth column, with the strand in the sixth column. The score value can really be any numerical value related to the associated interval.

ADD REPLYlink modified 2.2 years ago • written 2.2 years ago by Alex Reynolds27k

Oh yes the 5th column, thanks for the correction. But i do not see the point of this value if we do not know how it is computed... am I wrong? I need to use it to evaluate the quality of the peaks in my scoring function but i do not know at this point how much it is informative.

ADD REPLYlink written 2.2 years ago by fusion.slope200
1

It depends on the table you are pulling your BED data from. Each table should have an informational or schema page associated with it on the Genome Browser, which describes how the score field is calculated.

ADD REPLYlink written 2.2 years ago by Alex Reynolds27k
1

From ENCODE methods for peak calling of these cell lines:

https://www.encodeproject.org/experiments/ENCSR000AKB/

file "Description excerpt: Track description for UCSC Genome Browser composite track…"

SCORE: "Regions of statistically significant signal enrichment. The score associated with each enriched interval is the mean signal value across the interval. (Note that a broad region with moderate enrichment may deviate from the background more significantly than a short region with high signal.)"

is this score the one of the bed file? Am not sure..

ADD REPLYlink written 2.2 years ago by fusion.slope200

Am working with the CTCF files of ENCODE, for the dataset GM12878 (lymphoblastoid cell lines). I tried to search how the table was obtained but i did not find anything. If you have any idea about encode ChIP-seq dataset this will help me a lot. Thanks in advance Alex.

ADD REPLYlink written 2.2 years ago by fusion.slope200

I have edited 6th column to 5th column after Alex notification.

ADD REPLYlink written 2.2 years ago by fusion.slope200
1
gravatar for Devon Ryan
2.2 years ago by
Devon Ryan88k
Freiburg, Germany
Devon Ryan88k wrote:

The score can mean anything and be computed in any way. For ChIPseq it's usually some sort of peak score that's computed in a peak caller-specific manner.

ADD COMMENTlink modified 2.2 years ago • written 2.2 years ago by Devon Ryan88k

So there is not any technical foundation for this score? So why is it used?

ADD REPLYlink written 2.2 years ago by fusion.slope200
1

There's no predefined definition of the score, but the score in a given file from a given source will have a definition.

ADD REPLYlink written 2.2 years ago by Devon Ryan88k
0
gravatar for augustin.le_bouquin
18 months ago by
augustin.le_bouquin0 wrote:

I found this on the TopHat manual: in the output section junctions.bed. A UCSC BED track of junctions reported by TopHat. Each junction consists of two connected BED blocks, where each block is as long as the maximal overhang of any read spanning the junction. The score is the number of alignments spanning the junction. I understand that if you use Tophat, the score you see on each junction is the number of reads that spanning the junction.

ADD COMMENTlink written 18 months ago by augustin.le_bouquin0
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