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
