Phenotype Association Tools in Galaxy

Uploading a data file

The disease SNPs are available online, and we will use the Upload File tool in the Get Data section to add this to our Galaxy history. For this example we will use the URL method, which also works well with large files.

Type or paste the URLs in the large text box (red arrow):

  http://www.bx.psu.edu/miller_lab/docs/galaxy_phen_assoc/tutorial/cfHomVars.txt
  http://www.bx.psu.edu/miller_lab/docs/galaxy_phen_assoc/tutorial/cfHetVars.txt

You can paste both URLs in at once, each will be uploaded as a separate dataset. Also be sure to select the corresponding genome assembly in the Genome box. Typing in the select box will limit the list to items containing the specified text (e.g. "hg19"). We are going to select the interval format now (red arrow), so that we do not have to change the format after uploading as we did for the genomes. Then click Execute (green arrow) to upload the datasets into your history.

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