Dear Jim and Mary,
Thank you very much for your help, I just figured out that I need to specify track type as "bigBed 9" instead of "bigBed", and now it has all the coloring and controls on it. Have a great day! Xin On Thu, Jul 22, 2010 at 1:04 PM, Jim Kent <[email protected]> wrote: > 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
