Steps to convert IGB Quickload URL to UCSC track data hub URL

  1. In a web browser, navigate to https://translate.bioviz.org/
  2. In the URL text box, enter the IGB quickload URL you would like to convert.
    1. For example: https://api.bitbucket.org/2.0/repositories/lorainelab_udaya/testquickload/src/main/quickload1
  3. Click the "Do it" button to convert the track data hub URL.
    1. If successful, the converted URL will appear in the blue box.

View generated track hub in Ucsc

  1. In a web browser, navigate to https://genome.ucsc.edu/cgi-bin/hgHubConnect
  2. In URL text box, enter the generated track hub Url and click Add hub. 
    1. If successful, track hub can be viewed in Ucsc.

Structure of IGB Quickload for Track Hub Conversion 

       Example :  https://api.bitbucket.org/2.0/repositories/lorainelab_udaya/testquickload/src/main/quickload1

  1. TrackDb.txt
    1. File tags with no reference are considered to generate trackDb.txt 


      gnnots.xmltrackDb.txt
      title[0] (title splited by "/")
      track
      namebigdataurl
      title[-1]
      		shortLabel
      description
      		longLabel
      extension of name

      type 

      1. Follow below extensions for bigdataurl for specific type
        1. bigWig - 'bw', 'bigwig
        2. bigbed 12 - 'bb', 'bigbed'
        3. bigGenePred - '.bigGenePred.bb'
        4. bigChain - 'bigchain'
        5. bigNarrowPeak - '.bigNarrowPeak.bb'
        6. bigBarChart - '.bigNarrowPeak.bb'
        7. bigInteract - '.bigInteract.bb'
        8. bigPsl - '.bigPsl.bb'
        9. bigMaf - '.bigMaf.bb'
        10. hic - 'hic'
        11. bam - 'bam','cram'
        12. HAL - 'hal'
        13. vcfTabix - 'vcf', 'vcf.gz'

      		visibility (dense)
  2. genomes.txt

    1. genomes.txt can have only genome name and trackDb fields if the genome name matches with ucsc genome name

      genome.txt/annots.xmlgenomes.txt
      IGB genome name/ ucsc genome namegenome
      {genome_name}/trackDbtrackDb
      gets from species.txtorganism
      genome.txt defaultPos
      gets from annots.xml twoBitPath
  3. hub.txt

    1. It is a static data (Modifications to be done in future for better viewing)


      hub IGBQuickLoad
shortLabel IGB Quick Load
longLabel Track hub generated from IGB
genomesFile genomes.txt
email igbhelper@gmail.com