Hi, I got some progress from my side by the help from some other guy.. The real problem is that the gff file is not properly loaded into mysql database.. All introns are missing after the upload....
The program I used to upload the sequence is: ldHgGene <database> < table> <gff file> Best, Chen Hao ---------- Forwarded message ---------- From: Hao Chen <[email protected]> Date: Wed, Feb 16, 2011 at 10:10 AM Subject: Re: [Genome] how could I get the "fishbone" from trackDb.ra setting? To: Mary Goldman <[email protected]> Hi there, Thanks for your reply anyway but... http://genome.ucsc.edu do have what I mean "fishbone" in dense track.. sorry about the description which made more work... Here is two attachment of pictures.. One is what I mean "fishbone" and the other is the mirror genome browser I set up.. Hopefully it helps :) Best, Chen Hao On Tue, Feb 15, 2011 at 3:12 PM, Mary Goldman <[email protected]> wrote: > Hi Chen, > > I believe the "fishbone" you are talking about are the intron arrows. These > arrows do not display when any track is in dense - they are only visible in > squish, pack and full. I hope this information addressed your question and > was helpful. Please feel free to contact the mail list again if you require > further assistance. > > Best, > Mary > ------------------ > Mary Goldman > UCSC Bioinformatics Group > > > On 2/15/11 11:37 AM, Hao Chen wrote: > >> Hi, >> >> I am trying to set a mirror of UCSC browser here with Maize genome. >> >> fasta and GFF format files are used.. >> >> and then I modified trackDb.ra by adding a track: >> >> track Genes >> shortLabel Maize >> longLabel Maize_5a_Nov_2010 >> group genes >> priority 392 >> visibility dense >> color 120,10,130 >> type genePred refPred refMrna >> idXref refLink mrnaAcc name >> baseColorUseCds given >> baseColorDefault genomicCodons >> exonArrows on >> >> Everything works fine except that I can not see the "fishbone" when I am >> browsing in dense visibility..There are just thin and thick blocks.. >> Is there some setting about intron that I didn't notice? >> I was trying to find the solution from reading README file and searching >> on-line..but failed. >> >> Any help would be appreciated. >> >> Best, >> Chen Hao >> _______________________________________________ >> Genome maillist - [email protected] >> https://lists.soe.ucsc.edu/mailman/listinfo/genome >> >
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