You have input rows beyond the end of chr3 for danRer6. chrom chr3 size=60907308 numFeatures=2665 i=6107 start=61078861 end=61079631 numWindows=6091 i=6091 start=60912706 end=60912766 numWindows=6091 i=6091 start=60914044 end=60914190 numWindows=6091 i=6091 start=60914584 end=60914801 numWindows=6091 i=6091 start=60915135 end=60915195 numWindows=6091 i=6094 start=60944065 end=60944325 numWindows=6091 i=6094 start=60944715 end=60944775 numWindows=6091 i=6094 start=60945102 end=60945162 numWindows=6091 i=6099 start=60996629 end=60996689 numWindows=6091 i=6099 start=60997575 end=60997932 numWindows=6091 i=6099 start=60998342 end=60998834 numWindows=6091 i=6100 start=61006953 end=61007013 numWindows=6091 i=6106 start=61063211 end=61063271 numWindows=6091 i=6106 start=61064502 end=61064562 numWindows=6091 i=6106 start=61065020 end=61065324 numWindows=6091 i=6106 start=61068360 end=61068420 numWindows=6091 i=6106 start=61069681 end=61069771 numWindows=6091 i=6107 start=61070636 end=61070696 numWindows=6091 i=6107 start=61072792 end=61072852 numWindows=6091 i=6107 start=61075720 end=61075780 numWindows=6091 i=6107 start=61076827 end=61077377 numWindows=6091 i=6107 start=61077805 end=61077865 numWindows=6091 i=6107 start=61078424 end=61078484 numWindows=6091 i=6110 start=61108750 end=61108810 numWindows=6091 i=6111 start=61111930 end=61111990 numWindows=6091 i=6136 start=61362361 end=61363276 numWindows=6091 i=6136 start=61363615 end=61365794 numWindows=6091 i=6136 start=61366504 end=61366564 numWindows=6091 i=6167 start=61679273 end=61680154 numWindows=6091 i=6168 start=61679273 end=61680154 numWindows=6091 i=6209 start=62090652 end=62090712 numWindows=6091 i=6238 start=62380902 end=62380962 numWindows=6091 i=6238 start=62384074 end=62384134 numWindows=6091 i=6238 start=62388653 end=62388713 numWindows=6091 i=6238 start=62389732 end=62389792 numWindows=6091 i=6245 start=62458275 end=62458335 numWindows=6091 i=6287 start=62878953 end=62879013 numWindows=6091 i=6288 start=62881704 end=62881764 numWindows=6091 i=6289 start=62897677 end=62897737 numWindows=6091 i=6289 start=62898473 end=62898533 numWindows=6091
The GG code does not check these for invalid range since it assumes that was already done during CT upload/creation. We are checking into why the CT upload did not detect and report the problem. Meanwhile, you can proceed by fixing up the out-of-range rows. Finally, you will probably get better results if you make a GG input file. The process you are using to import a CT into GG will have two artifacts: 1. The bed score is converted to integer because the scores are supposed to be 0 to 1000 although it seems like some of the code tolerates negative integers. 2. The GG import is itself a windowed process whereby each 10k window is summed up. This might be fine for your application, but you should at least be aware of it. -Galt ----- Original Message ----- From: "Joseph Kingston" <[email protected]> To: [email protected] Sent: Saturday, July 31, 2010 2:38:12 PM GMT -08:00 US/Canada Pacific Subject: [Genome] Zebrafish Graph 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 _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
