Hi Maggie, The order of the optional fields in BED format is binding: lower-numbered fields must always be populated if higher-numbered fields are used. BED format is described here: http://genome.ucsc.edu/FAQ/FAQformat.html#format1
Right now your color designations are being interpreted as the name of the item, because it is the 4th field of data in your file. If you add some "filler" columns to your data so that the colors show up in the 9th field, you will see the colors you indicate. For example, this will display your first line (with the color changed from white to red): track name="Subject1" visibility=2 itemRgb="On" chr1 2158638 2158648 . 0 . 2158638 2158648 255,0,0 The name and strand fields will accept a "." and the score field can be 0. If you don't want to show any structure with thickStart and thickEnd, you can just repeat the chromStart and chromEnd columns. If you have further questions, please contact us again at [email protected]. -- Brooke Rhead UCSC Genome Bioinformatics Group On 5/1/12 4:12 PM, Cam, Maggie (NIH/NCI) [C] wrote: > Hi there, > > I'm trying to add a custom track that displays color bars, which at this > point doesn't really show any color besides black. Here is my file: > > track name="Subject1" visibility=2 itemRgb="On" > chr1 2158638 2158648 255,255,255 > chr1 2158915 2158925 255,255,255 > chr1 2159040 2159050 255,255,255 > chr1 2159351 2159361 255,255,255 > chr1 2159365 2159375 255,255,255 > chr1 2159369 2159379 255,255,255 > chr1 2159373 2159383 255,255,255 > chr1 2160249 2160259 255,255,255 > chr1 2160297 2160307 255,255,255 > chr1 2160666 2160676 255,255,255 > chr1 2161013 2161023 255,255,255 > chr1 2161049 2161059 255,255,255 > chr1 2161886 2161896 255,255,255 > chr1 2162001 2162011 255,0,0 > chr1 2162506 2162516 255,0,0 > chr1 2162682 2162692 255,255,255 > chr1 2162931 2162941 255,255,255 > chr1 2163437 2163447 255,0,0 > chr1 2163472 2163482 255,255,255 > chr1 2163529 2163539 255,0,0 > chr1 2164542 2164552 255,255,255 > chr1 2164602 2164612 0,255,0 > chr1 2165579 2165589 0,255,0 > chr1 2166155 2166165 0,255,0 > chr1 2169282 2169292 255,255,255 > chr1 2169407 2169417 255,255,255 > chr1 2170956 2170966 255,255,255 > chr1 2171212 2171222 255,255,255 > chr1 2171253 2171263 255,255,255 > chr1 2171834 2171844 0,255,0 > chr1 2173571 2173581 255,255,255 > chr1 2174725 2174735 255,255,255 > chr1 2174798 2174808 255,255,255 > chr1 2174895 2174905 255,255,255 > chr1 2179933 2179943 255,255,255 > chr1 2180027 2180037 255,255,255 > chr1 2180697 2180707 255,255,255 > chr1 2182126 2182136 0,255,0 > chr1 2182373 2182383 255,255,255 > chr1 2182612 2182622 255,255,255 > chr1 2183365 2183375 255,255,255 > chr1 2183438 2183448 255,255,255 > chr1 2185733 2185743 255,255,255 > chr1 2187457 2187467 255,255,255 > chr1 2188349 2188359 255,255,255 > chr1 2188767 2188777 255,255,255 > chr1 2188894 2188904 255,255,255 > chr1 2189027 2189037 255,255,255 > chr1 2190850 2190860 255,0,0 > chr1 2191299 2191309 255,255,255 > chr1 2191354 2191364 255,255,255 > chr1 2191402 2191412 255,255,255 > chr1 2191558 2191568 255,255,255 > chr1 2191658 2191668 255,255,255 > chr1 2193454 2193464 255,255,255 > chr1 2193741 2193751 255,255,255 > chr1 2194050 2194060 255,255,255 > chr1 2198760 2198770 255,255,255 > chr1 2198879 2198889 255,255,255 > chr1 2200890 2200900 255,255,255 > chr1 2200962 2200972 255,255,255 > chr1 2200984 2200994 255,255,255 > chr1 2201246 2201256 255,255,255 > chr1 2202028 2202038 255,255,255 > chr1 2202931 2202941 255,255,255 > chr1 2203012 2203022 255,255,255 > chr1 2203045 2203055 255,255,255 > chr1 2203589 2203599 255,255,255 > chr1 2203648 2203658 255,255,255 > chr1 2205213 2205223 255,255,255 > chr1 2205396 2205406 255,255,255 > chr1 2205498 2205508 255,255,255 > chr1 2205770 2205780 255,255,255 > chr1 2205824 2205834 255,255,255 > chr1 2205902 2205912 255,255,255 > chr1 2206662 2206672 255,255,255 > chr1 2207859 2207869 255,255,255 > chr1 2209140 2209150 255,255,255 > chr1 2209254 2209264 255,255,255 > chr1 2209341 2209351 255,255,255 > chr1 2209957 2209967 255,255,255 > chr1 2210335 2210345 255,255,255 > chr1 2211524 2211534 255,255,255 > chr1 2212997 2213007 255,255,255 > chr1 2213966 2213976 255,255,255 > chr1 2214240 2214250 255,255,255 > chr1 2216264 2216274 255,255,255 > chr1 2218432 2218442 255,255,255 > chr1 2218495 2218505 255,255,255 > chr1 2218549 2218559 255,255,255 > chr1 2219336 2219346 255,255,255 > chr1 2219932 2219942 255,0,0 > chr1 2220317 2220327 255,255,255 > chr1 2220497 2220507 255,255,255 > chr1 2221807 2221817 255,255,255 > chr1 2222253 2222263 255,255,255 > chr1 2222419 2222429 255,255,255 > chr1 2222440 2222450 255,255,255 > chr1 2222486 2222496 255,255,255 > chr1 2222674 2222684 255,255,255 > chr1 2224678 2224688 255,255,255 > chr1 2224791 2224801 255,255,255 > chr1 2225107 2225117 255,255,255 > chr1 2225139 2225149 255,255,255 > chr1 2225299 2225309 255,255,255 > chr1 2228160 2228170 255,255,255 > chr1 2228238 2228248 255,255,255 > chr1 2228319 2228329 255,255,255 > chr1 2229113 2229123 255,255,255 > chr1 2229140 2229150 255,255,255 > chr1 2230601 2230611 255,255,255 > chr1 2230640 2230650 255,255,255 > chr1 2230668 2230678 255,255,255 > chr1 2230923 2230933 255,255,255 > chr1 2231925 2231935 255,255,255 > chr1 2232063 2232073 255,255,255 > chr1 2232166 2232176 255,255,255 > chr1 2232469 2232479 255,255,255 > chr1 2232481 2232491 255,255,255 > chr1 2232527 2232537 255,255,255 > chr1 2234291 2234301 255,255,255 > chr1 2234433 2234443 255,255,255 > chr1 2234751 2234761 255,255,255 > chr1 2235375 2235385 255,255,255 > chr1 2235467 2235477 255,255,255 > chr1 2235655 2235665 255,255,255 > chr1 2236183 2236193 255,255,255 > chr1 2236443 2236453 255,255,255 > chr1 2236650 2236660 255,255,255 > chr1 2237185 2237195 255,255,255 > chr1 2237200 2237210 255,255,255 > chr1 2237543 2237553 255,255,255 > chr1 2237799 2237809 255,255,255 > chr1 2237991 2238001 255,255,255 > chr1 2238045 2238055 255,255,255 > chr1 2238334 2238344 255,255,255 > chr1 2238720 2238730 255,255,255 > chr1 2238895 2238905 255,255,255 > chr1 2238932 2238942 255,255,255 > chr1 2239065 2239075 255,255,255 > chr1 2239646 2239656 255,255,255 > chr1 2239768 2239778 255,255,255 > chr1 2240191 2240201 255,255,255 > chr1 2240324 2240334 255,255,255 > chr1 2240476 2240486 255,255,255 > > Thanks, > Maggie _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
