Hi Anthony, Were you thinking of a particular file format? You can color code in BED files (using the itemRGB attribute), and we also have a new Personal Genome SNP (pgSNP) file type that sounds a bit like what you are referring to (esp. in your second question, re: the two colored box).
BED files: http://genome.cse.ucsc.edu/FAQ/FAQformat.html#format1 Personal Genome files: http://genome.cse.ucsc.edu/FAQ/FAQformat.html#format10 I'll just give some brief description here. Maybe one of these will suit your needs. BED files with color coding If you upload the data in a BED file, the optional BED "itemRGB" attribute will allow you to color code allels. First, you'll want to set itemRGB="On" in the track line. Then in each row, you'll use the "name" field to identify the individual, and assign each individual, allele, or combination a color value in RGB. Here's an example data set with three individuals, with three different alleles assigned red, green and blue. If you display it in Pack, you'll see the individuals named, and a color corresponding to the allele. browser position chr7:127471196-127495720 browser hide all track name="ItemRGBDemo" description="Item RGB demonstration" visibility=2 itemRgb="On" chr7 127471196 127472363 Ind1 0 + 127471196 127472363 153,0,0 chr7 127472363 127473530 Ind1 0 + 127472363 127473530 153,0,0 chr7 127473530 127474697 Ind1 0 + 127473530 127474697 0,51,102 chr7 127474697 127475864 Ind2 0 + 127474697 127475864 153,0,0 chr7 127475864 127477031 Ind2 0 - 127475864 127477031 0,51,102 chr7 127477031 127478198 Ind2 0 - 127477031 127478198 0,51,102 chr7 127478198 127479365 Ind3 0 - 127478198 127479365 51,153,0 chr7 127479365 127480532 Ind3 0 + 127479365 127480532 0,51,102 chr7 127480532 127481699 Ind3 0 - 127480532 127481699 0,51,102 For more info on track color options: http://genome.cse.ucsc.edu/goldenPath/help/customTrack.html#TRACK http://genome.cse.ucsc.edu/goldenPath/help/customTrack.html#BED Personal Genome SNP Files These files can also do much of what you want. But you cannot choose colors. ACTG all have their own color and indels are shown in black. If you want the boxes 1/2 and 1/2 just put the same number for frequency "1,1". Please let me know if there's something else you were looking for not covered above. I can add it as a feature request. -- Greg Roe UCSC Genome Bioinformatics Group On 2/28/11 10:19 AM, Anthony Long wrote: > To whom it concerns: > > We want to serve up several custom tracks using the UCSC browser. Our > data consists of SNPs identified in a collection of resequenced inbred > strains (of Drosophila). Ideally we want a very compact > representation of SNPs where each "track" is a different individual > with SNP positions consisting of small square colored according to the > allele at that position. I do not see an easy way represent such a > track at present -- the current SNP track is more suited to population > aggregate information (such as the frequency of the SNP) -- but we are > interested in individual haplotypes. It would be nice if we could > chose among a dozen or so colors...(to represent indels etc in > addition to ACGT) > > A related track of great interest would have little squares (as above) > but allow for heterozygous individuals (e.g., a human HAPMAP > individual). Perhaps this could be accomplished via a subdivided > square where one half could be one color and the other another, with > several colors to chose from. > > > > I apologize if this is a silly questions but I do not see an easy way > to represent this data, and such a track would seem to be of interest > in any system where a core group of individuals are highly > characterized (e.g., human HAPMAP, Drosophila, mouse collaborative > cross, etc). If some track already exists perhaps all I need is a > point in the correct directions. > > Thanks. > > Anthony Long > Professor, Ecology and Evolution > U.C. Irvine > 92697-2525 > Ph: 949-824-2562 > http://cstern.bio.uci.edu > > > > > _______________________________________________ > Genome maillist [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
