View IGB Quickloads in UCSC Genome Browser

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 

• Folder{Genome_name}
  • annots.xml
  • genome.txt
• contents.txt

       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.xml	trackDb.txt
      title[0] (title splited by "/")	track
      name	bigdataurl
      title[-1]	shortLabel
      description	longLabel
      extension of name	type  Follow below extensions for bigdataurl for specific type bigWig - 'bw', 'bigwig bigbed 12 - 'bb', 'bigbed' bigGenePred - '.bigGenePred.bb' bigChain - 'bigchain' bigNarrowPeak - '.bigNarrowPeak.bb' bigBarChart - '.bigNarrowPeak.bb' bigInteract - '.bigInteract.bb' bigPsl - '.bigPsl.bb' bigMaf - '.bigMaf.bb' hic - 'hic' bam - 'bam','cram' HAL - 'hal' 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.xml	genomes.txt
      IGB genome name/ ucsc genome name	genome
      {genome_name}/trackDb	trackDb
      gets from species.txt	organism
      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