Hi Nadine, Your BED file is not formatted correctly. Note from our BED format instructions (http://genome.ucsc.edu/FAQ/FAQformat.html#format1): "The order of the optional fields is binding: lower-numbered fields must always be populated if higher-numbered fields are used."
If you want to use itemRgb, you'll need a 9 column BED file. Here's an example: track name="Name" description="Some Data" visibility=2 itemRgb="On" chr1 387780 1964453 1063778CHAK 0 + 0 0 255,0,0 chr1 1987443 6745820 1063778CHAK 0 + 0 0 255,0,0 chr1 143774595 246655340 1063778CHAK 0 + 0 0 0,0,255 chr1 112216670 118447882 1160638MORR 0 + 0 0 255,0,0 You can either zero-out the thickStart/End columns, like I have (the item will be drawn thick), or if you want them drawn thin you can use thickStart=thickEnd=chromStart. You can see more examples here: http://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html#BED Please let us know if you have any additional questions: [email protected] - Greg Roe UCSC Genome Bioinformatics Group On 10/10/11 4:56 PM, Nadine Berry wrote: > Dear UCSC, > > I am trying to colour my tracks red or blue but am having trouble getting the > browser to read my .bed file. I have a sample of my problem attached. > > I'm not sure if i need to write something different in the first line.... > > track name="MM" description="Clones" itemRgb="On" > or > > if i need to change the position of my columns so it can recognise the > "itemRgb="On'''' instruction. > > Any assistance would be greatly appreciated, > > Kind Regards, > > Nadine > > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
