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To submit BED data for analysis by GREAT, a client sends an HTTP GET request to http://greatbejerano.stanford.edu/great/public/cgi-bin/greatStart.php that includes:

  • requestURL (required) - The URL for the BED data to process.
  • requestSpecies (required) - The species assembly (e.g. hg18) corresponding to the BED data.
  • requestName (optional) - The name used to identify the BED data on the GREAT output page. If not given, "external data" is used.
  • requestSender (optional) - The name of the tool submitting the data, which is used as a prefix to requestName to identify the data on the GREAT output page.
  • bgURL (optional) - The URL for the BED data used as the background for the foreground/background test.
  • bgName (optional) - The name used to identify the background BED data on the GREAT output page. If not given, "external background data" is used.
  • outputType (optional) - The mode in which GREAT returns output.
    1. "web" - the standard GREAT UI for presentation in a browser (best for linking from an external website to GREAT)
    2. "batch" - a tab separated file for machine processing (best for script-powered analyses)

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Code Block
html
html
<html>
 <body>
  <a href="http://greatbejerano.stanford.edu/great/public/cgi-bin/greatStart.php?requestSpecies=hg18&requestName=Example+Data&requestSender=Client+A&requestURL=http%3A%2F%2Fwww.clientA.com%2Fdata%2Fexample1.bed">
  Send to GREAT
  </a>
 </body>
</html>

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Code Block
html
html
<html>
 <body>
  <a href="http://greatbejerano.stanford.edu/great/public/cgi-bin/greatStart.php?requestSpecies=hg18&requestURL=http%3A%2F%2Fwww.clientB.com%2Fdata%2Fexample2.php%3Ftf%3DNrsf">
  Send NRSF data to GREAT
  </a>
 </body>
</html>

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No Format
wget -O results.tsv "http://greatbejerano.stanford.edu/great/public/cgi-bin/greatStart.php?outputType=batch&requestSpecies=hg18&requestName=Example+Data&requestSender=Client+A&requestURL=http%3A%2F%2Fwww.clientA.com%2Fdata%2Fexample1.bed"

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  • Create a joblist of the format: outputFile queryURL where each line is a new job
    • EX:
      No Format
      results1.tsv http://greatbejerano.stanford.edu/great/public/cgi-bin/greatStart.php?outputType=batch&requestSpecies=hg18&requestName=Example+Data&requestSender=Client+A&requestURL=http%3A%2F%2Fwww.clientA.com%2Fdata%2Fexample1.bed
      results2.tsv http://greatbejerano.stanford.edu/great/public/cgi-bin/greatStart.php?outputType=batch&requestSpecies=hg18&requestName=Example+Data&requestSender=Client+A&requestURL=http%3A%2F%2Fwww.clientA.com%2Fdata%2Fexample2.bed
      
  • Then run ./greatBatchQuery.py joblist