Obtaining a reference genome from the UCSC Table Browser (GTF files)


Hello from GenomeSpace! In this video step, we will go over the process of obtaining a reference genome from the UCSC Table Browser. Launch UCSC Table Browser from GenomeSpace by clicking on the icon in the toolbar. The Table Browser is a one-stop access point for genomic reference sequence data. To access a specific dataset, we must narrow our search parameters. In this particular recipe, we set the ‘clade’ parameter to ‘other’ and the ‘output format’ to ‘GTF – gene transfer format’. The rest of the parameters should default
to our desired settings. Remember to specify an output file name,
such as ‘sacCer3_SGD.GTF’, and to check the GenomeSpace box to direct the output to your GenomeSpace account. Click ‘get output’ and wait for UCSC to display the successfully uploaded page. We now return to GenomeSpace
and refresh the page to view our
file in our top user folder. Feel free to move the file to any folder
you desire by clicking and dragging. Next, we will cover copying data from the GenomeSpace Public folder to a personal GenomeSpace account. Let’s start by navigating to the Public folder through the sidebar. Files shared as public can be accessed by any GenomeSpace user through the Public folder. From the Public folder make your way to SharedData, Demos, and finally Analysis Recipe 2. Copy the wild-type and mutant files to a personal GenomeSpace folder by clicking and dragging them to the folder in the sidebar. You can click and drag multiple files at
once by selecting a group of desired files first. Click ‘OK’ when the dialog box appears asking for confirmation Navigate to your personal folder to double-check that the copied files are there.

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