Hi Ken, To turn itemRgb on, you need to have the exact text: itemRgb="On" in your track line, as is demonstrated in the Example 5 BED track here: http://genome.ucsc.edu/goldenPath/help/customTrack.html#BED.
Yes, you will need to put in place-holding values for the fields for which you do not have information. Here are some example default values: 4. name: . 5. score: 0 6. strand: . 7. thickStart: chromStart 8. thickEnd: chromEnd 9. itemRgb: 0,0,0 We appreciate your suggestion for the modification of the BED specification and will pass this request on to our developers. Best, Mary ------------------ Mary Goldman UCSC Bioinformatics Group On 6/7/11 1:28 PM, Ken Weiss wrote: > I understand that to make each item in a custom track have its own > user-determined color (e.g., SNPs color-coded by minor allele frequency) one > needs to set itemRgb to on. But is it 'itemRgb=on', or must it have quotes > and/or capitalization as in itemRgb="On" ? > > Also since color is the 5th (or so) possible BED field, I understand that > the other fields need to be filled in. But sometimes there is no data or no > sense in these fields (such as strand +/-). Is it correct that you just put > in some place-holding values here? > > If that's the case, then I'd suggest a modification to the BED specs, so > that fields on doesn't want to use could be specified by * or something > rather than by guessing at what would hold the places but not affect the > track in an unwanted way. > > Thanks. > > Ken > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
