UCSC .bed file

[hsmart]

Hi All,

We have created a .bed file for UCSC browser. However, we would like to change score range from 0 to 20 instead of 0 to 1000. Can you please guild me how to do it?

Here is the more description of .bed file

http://genome.ucsc.edu/goldenPath/help/customTrack.html#BED

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:
shade
score in range ≤ 166 167-277 278-388 389-499 500-611 612-722 723-833 834-944 ≥ 945

Thanks,

Rakesh

[Thomas Doktor]

If it is just to get a color grading you could try multiplying all the scores in your bed file by 50. If you are viewing the track in full visibility, you can click on the track name itself and set a custom maximum score and then change viewing scaling to "use vertical viewing range setting". I don't know if this also changes the color grading profile if you're viewing the track in dense mode.

[Wei-HD]

Hi Thomas,

Can you please tell me if the score has some biological meaning?

Thanks!

[Thomas Doktor]

In this context the relevance of the score is usually to represent read depth. The actual biological meaning of this depends on the experiment you are performing, for instance the score and hence read depth in a ChIP-seq could reflect binding affinity, in an RNA-seq it could reflect expression levels and in a normal DNA-seq it could reflect copy number.