How To Change The Color Of Encode Tracks In Ucsc Browser?

Question

[Gireesh K. Bogu]

I played around with settings of ENCODE configuration but I couldn't able to locate color settings. Does any one know how to change the color of the ENCODE track ?

Thanx

[Gjain]

Gireesh, are you talking about UCSC genome browser? is this your data or some other data ...?

[Gireesh K. Bogu]

yes UCSC browser public ENCODE data.

[Giovanni M Dall'Olio]

I guess no, you can't... but you can play with the hgCart and see if you can make it work http://genome.ucsc.edu/cgi-bin/cartDump

[Ahdf-Lell-Kocks]

I would also very much like to be able to do this!

Answer 1

[Gjain]

Hi Gireesh,

As Giovanni mentioned, there is no such capability to do that for now. But if you really want to see different color tracks, you can download the data from the table browser in the bed format and modify it.

for example:

track name="ItemRGBDemo" description="Item RGB demonstration" visibility=2
itemRgb="On"
chr7    127471196  127472363  Pos1  0  +  127471196  127472363  255,0,0
chr7    127472363  127473530  Pos2  0  +  127472363  127473530  255,0,0

It is also possible to color items by strand in a BED track using the colorByStrand attribute in the track line as shown below.

track name="ColorByStrandDemo" description="Color by strand demonstration"
visibility=2 colorByStrand="255,0,0 0,0,255"
chr7    127471196  127472363  Pos1  0  +
chr7    127475864  127477031  Neg1  0  -

you can find more information here.

[Gireesh K. Bogu]

@Gjain: Thanx. Yes I know this but it would be more easier if we can change the color of the directly it self. One of the main limitation with your approach is the size of the datasets that need to be both downloaded and uploaded.

[Gjain]

I agree but that`s why I said "if you really want".