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The Cancer Genomics Hub (CGHub) Exit Disclaimer logo is a secure repository for storing, catalogueing, and accessing cancer genome sequences, alignments, and mutation information from The Cancer Genome Atlas (TCGA) consortium project and other cancer related projects.

The mission of CGHub is to facilitate the work of scientific researchers. CGHub is designed to be a fully automated resource, appearing to users as an extension of their home institute computing resource. User scripts employ the CGHub Application Programming Interface (API) Exit Disclaimer logo to retrieve the CGHub catalog (index) of files; to select files for download based on metadata attributes such as cancer type, sequence type, source sequencing center or date range; then to initiate download, and finally to confirm success. CGHub is managed by the University of California, Santa Cruz (UCSC), under a subcontract from SAIC-Frederick.

For more information about CGHub, visit the About CGHub Exit Disclaimer logo webpage.

For customer support related issues or to sign up for the “CGHub Announce” email list, email CGHub Support at: support@cghub.ucsc.edu. The CGHub Announce list is a very low volume email feed, where you can stay up-to-date with any scheduled service related outage and the latest news releases for CGHub. For additional news and updates on CGHub, visit the CGHub News Exit Disclaimer logo page.

The CGHub Help Exit Disclaimer logo page displays all of the available documentation for CGHub, such as the CGHub User's Guide Exit Disclaimer logo , and Technical Manual Pages Exit Disclaimer logo for GeneTorrent. The help page also displays Troubleshooting Exit Disclaimer logo and Frequently Asked Questions (FAQ) Exit Disclaimer logo links.

To download or upload TCGA data (BAM files)  from CGHub, you must be granted authorization from the Data Access Committee (DAC). Visit the “new user Exit Disclaimer logo ” area for helpful information on the steps you must complete to gain access to the BAM files stored at CGHub. To see a list of controlled access and public access datasets hosted at CGHub, see the CGHub “data sets” page.

Once you have been granted authorization to download or upload data, you must install CGHub’s GeneTorrent software. GeneTorrent is the software for downloading data, and cgsubmit is the software used to upload data. Both can be found on the downloads Exit Disclaimer logo page.  

  • As of February 2013, CGHub now supports Windows and Mac operating systems, in addition to the previously supported Linux platforms.

In addition, CGHub offers various ways to search their publicly available metadata.

  • CGHub has released a web based data browser, which allows users to build a manifest.xml file which users can pass to the GeneTorrent program to download BAM files, or the query results can be downloaded as a metadata.xml for examination. See the CGHub Data Browser  Exit Disclaimer logo website for more information. For technical details on the Data Browser, see the Data Browser Specifications.
  • cgquery queries CGHub’s data and is designed to be used in conjunction with GeneTorrent (GT), and is included with the GT software package (see the Downloads  Exit Disclaimer logo page for more information and to download GeneTorrent). With cgquery, you can create an output XML file to pass to GeneTorrent to download multiple BAM files. Cgquery can also be executed on its own, if you just want to study the metadata. See the CGHub User’s Guide  Exit Disclaimer logo for more information and usage examples.
  • The Summary Statistics  Exit Disclaimer logo page is a nice overview of the data stored at CGHub.

If you have additional questions about CGHub, contact CGHub Support at: support@cghub.ucsc.edu.

Help Downloading Files

For help accessing PDF, RTF, MS Word, Excel, PowerPoint, audio, or video files on this wiki, go to Help Downloading Files.

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