This and Exercises 2 and 3 are part of an Galaxy-sponsored free introductory OpenHelix tutorial accessed here.
Obtain UCSC Genome Browser data using the Galaxy interface. Examine the data, and begin to prepare the data for subsequent analyses by editing attributes.
1. Access the Galaxy site (http://galaxy.psu.edu), and click on Go to our public site in the top green box area.
2. Click on the “Get Data” link in the left Tools area to expand that topic. Click UCSC Main.
3. On the right frame the UCSC Table Browser interface will be displayed. Make these changes to the UCSC interface: In clade choose “Mammal,” “Human” and “Mar. 2006” for assembly. In group: choose Variation and Repeats and for Track choose “SNPS (130).” (primary data table, “snp130”, will be set automatically for you) In region: move radio button to position, and clear out the default location. Enter BRCA1 in the text box. Click lookup. From the results list choose the first BRCA1 item (uc010cza.1) at the top by clicking on it. Its position will display back in the position box. Leave any other menu settings as default at this time.
4. Leave the output format menu set to “BED – Browser extensible Data”. Check the box “Send output to Galaxy”.
5. Click the “get output” button near the bottom of the form.
6. The next page to load offers a “Send query to Galaxy” button. Leaving all as default, click that button.
7. You should now have an item in your history on the right side. It starts of grey or yellow, and will turn green when complete.
8. Click the title hyperlink to examine the summary data.
9. Click the pencil icon to be able to prepare the data set for subsequent analyses.
10. Click the eyeball icon to view the data in the center panel area.
11. Change the name to: BRCA1 SNPs.
12. Click the “Save” button at the lower area of the center panel.
13. Your file has been renamed and the interface will indicate that your attributes have been updated. Change the history name to “BRCA1 SNPs Flanking” by clicking the pencil icon next to the words “unnamed history” and typing those words, hit enter. Ifyou are registered and signed in, you can add tags by clicking the text “0 tags” and start typing. Add “snps” and then a space, and “brca1” and then a space.
The dataset you have uploaded to Galaxy in this exercise will look like this. Use this dataset in exercise 2. You could also just import this dataset (click green "+" to import to your account) and skip steps 1-12 here and go directly to exercise 2 :