Importing files from the BX Browser

We will start by importing a dataset from PSU's BX table browser, which is a partial mirror of the UCSC Main table browser that specializes in personal genomes. In the Tools panel on the left, click on the section called Get Data to open it, then click on the BX Table Browser tool (indicated by a red arrow in the screenshot below). In general the input form for the selected tool will appear in the center panel, along with other information about the tool. In this case, Galaxy takes us to the external server's own interface to make our selections. Here we have temporarily hidden Galaxy's history panel on the right to make more room for the form.

First make sure the genome and assembly are correct; for this example we want Human build hg19. We want the group "Personal Genomes", track "1000 Genomes 2012", and table "CEU (1000Genomes2012CEU)", which are all shown in the red box below. For the region option, we want the SNPs from the whole genome (red arrow). The default output format is BED, and often that is a good choice, but in this case we want to keep the data in its initial pgSnp format in order to obtain the frequency information. Choose "selected fields from primary and related tables", because we need to omit one of the columns. Since we arrived here via Galaxy, the box for sending the output back to Galaxy is already selected by default. When done, click the "get output" button (green arrow).