Hi Myriam, I see what is happening now. To upload a file directly to Genome Graphs, it must be in one of the formats listed here:
http://genome.ucsc.edu/goldenPath/help/hgGenomeHelp.html#Format Your file contains wiggle data, which cannot be loaded into Genome Graphs, but whic can be loaded into a custom track. If you go to the custom track page (http://genome.ucsc.edu/cgi-bin/hgCustom) and load your file successfully there, you can then go to Genome Graphs and choose to "import" the data in your custom track. Your original data will be converted into a custom track of type chromGraph using a window-size of 10,000 bases. The process of importing a track is described here: http://genome.ucsc.edu/goldenPath/help/hgGenomeHelp.html#Import I did try uploading your file directly to Genome Graphs, and I got the very confusing message: "Data Upload Complete (6941057 bytes) These data are now available in the drop-down menus on the main page for graphing." This message should be changed to let users know that data was in fact not successfully uploaded. I will forward this problem to our developers. -- Brooke Rhead UCSC Genome Bioinformatics Group On 11/03/08 05:28, Myriam Saida wrote: > Hi Brooke, > > Thank you for answering. I have tried the reset step you suggested and > after loading your exemple data, I could visualise them. However, with > my data, it still doesn't work. I upload them as a txt file (and I name > them in the right box) by clicking on the "upload" button and it says > that my data were uploaded ok and that they can be displayed back on the > main menu. Once I click the "OK" button which send me back to the main > Genome Graphs menu, my data are just not there on the graph drop-down > menu next to the word "graph". > Please find enclosed my data (sorry it is quite big). They are CGH array > data. The first column is the chromosome, the second and third columns > are respectively the probe start and end, and the fourth and last column > is the value associated to each probe on the array (here, a log ratio of > dye intensity). > > Thank you so much! > > Best regards, > > Myriam Saida > > > > > Quoting Brooke Rhead <[EMAIL PROTECTED]>: > >> Hello Myriam, >> >> The tool seems to be working correctly from here, so can you give me >> more details on the exact steps you are using? >> >> Are you uploading data as a file, from a URL, or by pasting data >> directly into the box on the "Upload Data to Genome Graphs" page? >> >> Are you entering a name for the data set on that page, or leaving it >> blank? If you leave the box blank, a name will be assigned to it: >> "User Track +1". If you are using a name that you have used >> previously, the data in the track will be overwritten with the latest >> version. >> >> Once the data is uploaded, the name should appear back on the main >> Genome Graphs page in the drop-down menu next to the word "graph". >> >> If nothing appears for your data in particular, please send me a sample >> of the data directly (no need to cc the whole mailing list), and we >> will try to reproduce the problem here. >> >> If nothing appears in the graph drop-down menu for even our sample set >> of data: >> http://genome.ucsc.edu/goldenPath/help/hgGenomeHelp.html#Sample >> http://genome.ucsc.edu/goldenPath/help/hgGenome_example1.txt >> >> then can you tell me what web browser and version you are using >> (Internet Explorer 7, Firefox 3.0, etc.) and on what platform (Windows, >> Mac, Linux, etc.)? >> >> Finally, it is possible that a "cart reset" might help. We use a cart >> to keep track of the Genome Browser settings that you select, and >> sometimes the cart gets into a mixed-up state. You can reset the cart >> by going to this url: >> >> http://genome.ucsc.edu/cgi-bin/cartReset >> >> Be aware that all of your settings, including custom tracks, will be >> lost if you reset your cart. >> >> -- >> Brooke Rhead >> UCSC Genome Bioinformatics Group >> >> >> On 10/31/08 02:35, Myriam Saida wrote: >>> Hello, >>> >>> I am having trouble to use the genome graph program. After I load >>> my data (and after getting the confirmation message from the >>> program that they are uploaded ok), I can not visualise them on >>> graph, i.e. there is nothing to select on the graph drop-down menu >>> and it tells me there is no graph selected for the assembly and >>> that I should upload data which I have just done. I have even tried >>> the tutorial on the help pages and I have the same problem. Do you >>> have any hints on what is going wrong? >>> >>> Thanks, >>> >>> Myriam Saida >>> > > > > _______________________________________________ Genome maillist - [email protected] http://www.soe.ucsc.edu/mailman/listinfo/genome
