Did you try pack mode as well as dense? On Jul 22, 2010, at 4:16 PM, Xin Zhou wrote:
> Dear Mary, > > > Thank you for your reply! > > > I'm working on a local mirror of UCSC browser and want to use bigBed > instead of bed9 for some huge read-alignment track files. Following is > the .as file for autoSql commands, it matches my bed9 format, I think: > > > table hg18KGchr7 > "UCSC Genes for chr7 with color plus GeneSymbol and SwissProtID" > ( > string chrom; "Reference sequence chromosome or scaffold" > uint txStart; "Transcription start position" > uint txEnd; "Transcription end position" > string name; "Name of gene" > uint score; "Score" > char[1] strand; "+ or - for strand" > uint cdsStart; "Coding region start" > uint cdsEnd; "Coding region end" > string color; "Green on + strand, Red on - strand" > ) > > > > And the track definition for the bigBed tracks contain following lines: > > type bigBed > itemRgb on > > > I actually used composite track feature, and I added above lines at > each level of definition. I hope that wouldn't matter. And I still > cannot get the bed9 style control and coloring. > > > Thank you! > > > Xin > > > On Wed, Jul 21, 2010 at 5:31 PM, Mary Goldman <[email protected]> wrote: >> Hi Xin, >> >> My best guess is that track line isn't configured quite right. Did you >> include 'type=bigBed' in your track line? Also, to see color in the squish, >> pack and full modes you will need to include 'itemRgb="On" ' in the track >> line as well. Another possibility is that your 9 fields don't line up with >> those specified in bedExample2.as. Have you looked at this file and verified >> that it matches your fields? >> >> I hope this helps you solve your problem. If none of these solutions work, >> please reply with the track and browser lines that you used to upload your >> custom track. >> >> Thank you, >> Mary >> ------------------ >> Mary Goldman >> UCSC Bioinformatics Group >> >> On 7/21/10 10:59 AM, Xin Zhou wrote: >>> >>> Hi all, >>> >>> >>> I converted bed 9 format file into bigBed using following command: >>> >>> $ bedToBigBed -as=bedExample2.as -bedFields=9 in_file chr_size out_file >>> >>> And made the bigBed file visible on browser. The problem is, the bed 9 >>> effects are missing (strand, coloring), and view options only include >>> "full", "dense", "hide". >>> >>> Is it possible to tweak it so to get bed 9 effect from bigBed track? >>> >>> >>> Thanks! >>> >>> >>> Xin Zhou >>> _______________________________________________ >>> Genome maillist - [email protected] >>> https://lists.soe.ucsc.edu/mailman/listinfo/genome >>> >> > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
