b089078d975056489840af38badc2598592bc47f dschmelt Mon Apr 15 14:15:57 2019 -0700 Fixing weird double quotes character #23317 diff --git src/hg/htdocs/goldenPath/help/bigGenePred.html src/hg/htdocs/goldenPath/help/bigGenePred.html index ec79cb3..d911d7e 100755 --- src/hg/htdocs/goldenPath/help/bigGenePred.html +++ src/hg/htdocs/goldenPath/help/bigGenePred.html @@ -223,31 +223,31 @@
  • Convert the GTF file to genePred extended format using the gtfToGenePred command.
    gtfToGenePred -genePredExt bigGenePredExample4.gtf example4.genePred
  • Convert the genePred extended file to a pre-bigGenePred text file.
    genePredToBigGenePred example4.genePred bigGenePred.txt
  • Obtain helper files for the conversion from pre-bigGenePred to binary bigGenePred.
    wget http://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/hg38.chrom.sizes
     wget http://genome.ucsc.edu/goldenPath/help/examples/bigGenePred.as
  • Convert your text bigGenePred to a binary indexed format.
    bedToBigBed -type=bed12+8 -tab -as=bigGenePred.as ex4BigGenePred.txt hg38.chrom.sizes bigGenePred.bb
  • Put your binary indexed file in a web-accessible location. See the - hosting section for more information.
  • + hosting section for more information.
  • View your dataset in the Browser by entering your hosted data URL in the bigDataUrl field of the URL. For example, you can paste this link into your web browser.
     http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg38&hgct_customText=track%20type=bigGenePred%20bigDataUrl=http://genome.ucsc.edu/goldenPath/help/examples/bigGenePred.bb
    You can also add your data in the custom track management page. This allows you to set position, configuration options, and write a more complete desciption. If you want to see codons, you can right click, then click configure codon view or set these options using the baseColorDefault=genomicCodons code as is done below.
    browser position chr19:44905795-44909393 
     track type=bigGenePred baseColorDefault=genomicCodons name="bigGenePred Example Four" description="BGP Made from genePred" visibility=pack bigDataUrl=http://genome.ucsc.edu/goldenPath/help/examples/bigGenePred.bb
  • Sharing your data with others

    If you would like to share your bigGenePred data track with a colleague, learn how to create a URL link to your data by looking at Example #6.