Thank you for your help Jennifer. I tried the steps you suggested with some success. When I import one chromosome at a time it imports just fine. However, when I try to add the entire genome as a custom track and then import the genome I just get stuck on the following message.
Table Import in Progress It just sits there forever. Is there some limit on the amount of data I can import? The genome I am importing is 2.2MB of data in the following format: browser position chr1:44006-44066 track name="leukemia_immatureT" #Chromosome StartPosition EndPosition RegionName Score chr1 44006 44066 region_0 0.727264185479 chr1 46023 46083 region_1 0.560017387231 chr1 47390 47601 region_2 2.02842618698 chr1 48251 48311 region_3 0.0196590689408 The entire file is also attached to this email if you want to try it yourself. Thank you for your help. Joseph ----- Forwarded Message ---- From: Jennifer Jackson <[email protected]> To: Joseph Kingston <[email protected]> Cc: [email protected] Sent: Tue, July 27, 2010 9:19:50 PM Subject: Re: [Genome] Zebrafish Graph Hello Joseph, I am wondering if there is some confusion about using the "upload" vs the "import" function? It is easy to mix the two up. The "upload" function has a limited set of input formats. However, if you use "import", then many file types are accepted. This would include a BED file that has been already loaded as a custom track. This is what you should do for your case: 1) load your BED file as a custom track from the target assembly's gateway page, using the button "add custom track" 2) back in Genome Graphs, now use the "import" function (hint: find your data in the very first track group called "Custom Tracks") 3) after import, the custom track dataset will come up in the drop down menu on the main Genome Graph's home page. I just tested your data and this worked fine in the Zebrafish Dec. 2008 (Zv8/danRer6) assembly. Hopefully it will work for you as well, but please let us know if you need more help, Jen UCSC Genome Browser Support On 7/27/10 4:34 PM, Joseph Kingston wrote: > Greetings again, > > I am trying to upload data into the Genome Graphs tool using BED file format >and > I still can't get it to work. Even the example data provided in the FAQ will >not > upload. It doesn't show any error message at all. It says it uploaded >completely > but --nothing-- appears in the drop down list. This is a sample of the data I >am > trying to upload, is there anything wrong with it? > > track name=pairedReads description="Clone Paired Reads" useScore=1 > chr1 44006 44066 region_0 564 > chr1 46023 46083 region_1 672 > chr1 47390 47601 region_2 760 > chr1 48251 48311 region_3 31 > chr1 80315 80375 region_4 171 > chr1 83080 83140 region_5 18 > chr1 84485 84545 region_6 200 > > > Joseph > > > ----- Forwarded Message ---- > From: Jennifer Jackson<[email protected]> > To: Joseph Kingston<[email protected]> > Cc: [email protected] > Sent: Mon, July 26, 2010 7:11:03 PM > Subject: Re: [Genome] Zebrafish Graph > > Hello Joseph, > > The Genome Graph's function requires specific input formats. The format > that you are loading is not in this set (BED4). > > This help page linked off the Genome Graph's home page can help: > http://genome.ucsc.edu/goldenPath/help/hgGenomeHelp.html > > Specifically, see the sections about Formatting Data and the Examples. > > Please feel free to contact the mailing list support team again if you > would like more assistance. > > Warm regards, > > Jen > UCSC Genome Browser Support > > On 7/26/10 5:19 PM, Joseph Kingston wrote: >> Hello, >> >> I am a first time user of Genome Graphs. I am trying to upload my own data > into >> Genome Graphs but it seems to have no effect. The options I choose are as >> follows: >> Clade: Vertebrate >> genome: Zebrafish >> assembly: Zv8 >> >> Then I click upload and paste in the data included below (leaving all other >> fields unchanged). I submit the form to get the following "Data Upload >> Complete" >> message. However, on the 'graph' drop-down list my upload is not shown. It is >> just a list with --nothing-- in it. Is there something wrong with the data I > am >> uploading? >> >> Data Upload Complete (1559 bytes) >> >> >> >> These data are now available in the drop-down menus on the main page for >> graphing. >> >> Thank you for your help, >> Joseph >> >> ________________________________ >> browser position chr1:44006-44066 >> track name="input_immatureT" >> #Chromosome StartPosition EndPosition RegionName Score >> chr1 44006 44066 region_0 564 >> chr1 46023 46083 region_1 672 >> chr1 47390 47601 region_2 760 >> chr1 48251 48311 region_3 -31 >> chr1 80315 80375 region_4 -171 >> chr1 83080 83140 region_5 -18 >> chr1 84485 84545 region_6 200 >> chr1 164425 164485 region_7 557 >> chr1 165078 165138 region_8 887 >> chr1 174603 174663 region_9 401 >> chr1 201776 201836 region_10 -592 >> chr1 205894 205954 region_11 234 >> chr1 206899 206959 region_12 -95 >> chr1 269936 270155 region_13 841 >> chr1 272603 272663 region_14 450 >> chr1 273072 273132 region_15 804 >> chr1 274649 274709 region_16 135 >> chr1 303976 304036 region_17 33 >> chr1 495304 495364 region_18 91 >> chr1 502144 502204 region_19 445 >> chr1 503071 503131 region_20 390 >> chr1 562783 563017 region_21 790 >> chr1 581465 581755 region_22 -168 >> chr1 673678 673738 region_23 -159 >> chr1 676089 676149 region_24 148 >> chr1 1463640 1463700 region_25 31 >> chr1 2055855 2055915 region_26 648 >> chr1 2056770 2056830 region_27 529 >> chr1 2058602 2058662 region_28 -55 >> chr1 2238513 2238573 region_29 259 >> chr1 2447697 2447757 region_30 908 >> chr1 2451604 2451664 region_31 -184 >> chr1 2509550 2509824 region_32 638 >> chr1 2512283 2512343 region_33 178 >> chr1 2559324 2559384 region_34 272 >> chr1 2561162 2561222 region_35 -2 >> chr1 2561726 2562576 region_36 -162 >> chr1 2562954 2563014 region_37 -70 >> chr1 2564525 2564585 region_38 122 >> chr1 2564868 2564928 region_39 87 >> chr1 2566578 2566638 region_40 -82 >> chr1 2566962 2567022 region_41 327 >> >> >> >> >> _______________________________________________ >> Genome maillist - [email protected] >> https://lists.soe.ucsc.edu/mailman/listinfo/genome > > > > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome
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