Hello Peng, For BED format files, the answer is yes for both. For wiggle, color can be specified, and positive and negative values (or where you place the Y-axis) can be two different colors, but there is no shading, the variation along the X-axis in a wiggle graph represents the value assigned to the data point. See the links and examples below or check out some of the current browser tracks with these formats and compare to determine the best format to model your dataset.
BED: The values of the score field specifies the color by grey scale - so if two tracks have the same value, the color will be the same. Items can be set to specific colors using the itemRgb field. http://genome.ucsc.edu/FAQ/FAQformat http://genome.ucsc.edu/FAQ/FAQformat#format1 WIG: Wiggle, bigWig, and bedGraph formats also allow color specification. http://genome.ucsc.edu/FAQ/FAQformat#format6 Thanks, Jennifer ps: Any follow-up questions should be sent directly the genome mailing list for the fastest response over the next two weeks. ------------------------------------------------ Jennifer Jackson UCSC Genome Bioinformatics Group > > Subject: How to show multiple tracks with the same color map (dense > visibility)? > Sent By: "Peng Yu" <[email protected]> > On: December 19, 2009 9:41 AM > To: [email protected] > > ~~~~~~~~~~~~~~~~~~~~~~~~~~~ > > I want to show multiple tracks (eg. the following one). The same gray > scale represent different values in different tracks. Is there a way > to use the same gray scale for the same value in different tracks? Is > there a way to use different color rather than gray scale? > > > > browser position chr1:100-130 > browser hide all > browser pack refGene encodeRegions > browser full altGraph > track type=bedGraph name="name1" description="description1" > visibility=dense > chr1 101 102 1 > chr1 111 112 2 > chr1 121 122 3 > track type=bedGraph name="name2" description="description2" > visibility=dense > chr1 101 102 -1 > chr1 111 112 -2 > chr1 121 122 -3 _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
