Hello Latha, The bugs that were found in the Agilent CGH244A track have been resolved, and the updated track was made available last Friday (1/23). I tried uploading the sample data you included on the regular site (not the test site). The upload worked just fine, but because it was such a small sample, it was almost invisible on the Genome Graphs display. The sample data appears as a small dot near the beginning of chromosome 1. If you are still unable to upload data on the main site, and if the small data set does not explain the apparent unsuccessful upload, please let us know.
> Also we would like to know how we can make this approach work for > data whose marker information is not in the UCSC database? You can use the "chromosome base" format: http://genome.ucsc.edu/goldenPath/help/hgGenomeHelp.html#FormatUpload Alternatively, you can make a custom track in the Genome Browser, and then use the "import" button rather than the "load" button in Genome Graphs to view the data there. It sounds like this option might work better for your needs. > The next issue we have is that once we have the data on the genome > graph, we go to the Chromosomal view but we are unable to see any > annotation information upon clicking the data on the chromosomal > view. The custom track created by Genome Graphs is a continuous format, and as such, there is not a way to annotate each data point from the original set of markers you uploaded. You can, however, enter a short description for the track created with Genome Graphs: http://genome.ucsc.edu/goldenPath/help/hgGenomeHelp.html#Upload If you want to start instead by creating a custom track in the Genome Browser, there *is* a way to add annotations for each item in the track. See: http://genome.ucsc.edu/goldenPath/help/customTrack.html , scroll to "Step 5. (Optional) Add details pages for individual track features" You can then import the custom track into Genome Graphs. This will create a second, continuous-format custom track that will display alongside the discrete-format custom track you created. I hope this information helps you use the UCSC tools effectively. -- Brooke Rhead UCSC Genome Bioinformatics Group On 01/26/09 19:30, Ramdas,Latha wrote: > Hi > Please let us know if the issue of the track for Agilent CGH244A has been resolved. I have attached a powerpoint file showing the workflow we think is right to show custom data on the Human Genome Graph. I tried this for the Agilent CGH 244A marker track using your test server. This is still not working on the UCSC Genome Browser page. > The work flow that I have described in the .ppt file is what we plan to implement in a programatic way. We have the UCSC browser and some of the databases locally downloaded and we plan to use this for our data display. Please let us know when the above issue will be solved so we can update our download. Also we would like to know how we can make this approach work for data whose marker information is not in the UCSC database? The next issue we have is that once we have the data on the genome graph, we go to the Chromosomal view but we are unable to see any annotation information upon clicking the data on the chromosomal view. Please help in streamlining this. If you need more information, please contact me. > > Appreciate your help. > Thank you > > > ---------------------------------------------- > Latha Ramdas, Ph.D > Scientific Application Specialist > Research IS & Technology Services > M D Anderson Cancer Center > Houston, TX 77030 > Ph: 713 794 5924; > Fax: 713 563 4750; > Pager:713 606 4159 > [email protected] > > > > -----Original Message----- > From: Pauline Fujita [mailto:[email protected]] > Sent: Tuesday, January 20, 2009 7:45 PM > To: Ramdas,Latha > Cc: '[email protected]' > Subject: Re: [Genome] Genome Graph on UCSC browser > > Hello Latha, > > We recently found new issues with these tracks and are currently in the > process of resolving them. They should be up in the near future. Thank > you for your continued patience. > > Best regards, > > Pauline Fujita > UCSC Genome Bioinformatics Group > http://genome.ucsc.edu > > > Ramdas,Latha wrote: >> Is this issue resolved? >> >> Thanks >> >> ************************************************************** >> Latha Ramdas, Ph.D >> Scientific Application Specialist >> Research IS & Technology Services >> University of Texas M D Anderson Cancer Center >> Houston, TX 77030-4009 >> email: [email protected] >> Ph: 713 794 5924 >> Fax: 713 563 4750 >> >> >> >> >> -----Original Message----- >> From: Brooke Rhead [mailto:[email protected]] >> Sent: Friday, January 16, 2009 12:08 AM >> To: Ramdas,Latha >> Cc: '[email protected]' >> Subject: Re: [Genome] Genome Graph on UCSC browser >> >> Hello Latha, >> >> This track was temporarily removed from the Genome Browser. See this >> previously-answered question for details: >> >> http://www.soe.ucsc.edu/pipermail/genome/2009-January/017938.html >> >> Sorry for the inconvenience. We are working to get the track restored. >> >> -- >> Brooke Rhead >> UCSC Genome Bioinformatics Group >> >> On 01/15/09 18:24, Ramdas,Latha wrote: >> >>> I am trying to upload a copy number analysis data file from Agilent >>> >> Human Genome CGh microarray 244A on to the Human Genome graph . I pick >> the marker type as Agilent CGH 244a. However when I submit the data, I >> get the following error message: >> >>> 'Sorry, no data for Agilent CGH 244A on this assembly.' Is the >>> information for the Agilent CGH 244A in your database. Why is >>> >> the data not displayed on the Genome graph view. >> >>> A quick response will be greatly appreciated. > >>> ---------------------------------------------- >>> Latha Ramdas, Ph.D >>> Scientific Application Specialist >>> Research IS & Technology Services >>> Ph: 713 794 5924; >>> Fax: 713 563 4750; >>> Pager:713 606 4159 >>> [email protected]<mailto:[email protected]> >>> >>> >>> >>> _______________________________________________ >>> Genome maillist - [email protected] >>> http://www.soe.ucsc.edu/mailman/listinfo/genome >>> >> _______________________________________________ >> Genome maillist - [email protected] >> http://www.soe.ucsc.edu/mailman/listinfo/genome >> > _______________________________________________ Genome maillist - [email protected] http://www.soe.ucsc.edu/mailman/listinfo/genome
