This and Exercises 1 and 3 are part of an Galaxy-sponsored free introductory OpenHelix tutorial accessed here.
Exercise 2: exercise 1 dataset is needed to complete this exercise
Obtain 50bps of flanking sequence from SNPs obtained in exercise 1
1. You will need to obtain the flanking region and then sequence of the SNPs you downloaded in exercise 1. If you are doing this exercise immediately after exercise 1, the data will be in your history. If not, go to the “Options” pull down menu at the top of the history column and click “Saved Histories.” Your previously created history “BRCA1 SNPs Flanking” will be there. Click on the title and pulldown menu, click “Switch” to add history to your current analysis.
2. First, get the flanking region of these SNPs. In the left Tools column, click the heading “Operate on Genomic Intervals.” Then click on the tool “Get Flanks...”.
3. The options for getting the flanking regions will appear in the middle column. Change the “Location of the flanking region/s” menu to “both” (alternately you could have chosen either upstream or downstream). Leave all the rest of the options as default (Select Data: BRCA1 SNPs, Region: Whole Feature, Location of Flanking region: both, Offset: 0, Length of flanking region: 50). Click “Execute.”
4. This will result in a second dataset with locations of 50bp upstream of each SNP. Now obtain the sequence of these locations. In the left column, click the heading “Fetch Sequences.” Click the tool “Extract Genomic DNA.”
5. The options appear in the middle column. Make sure “2: Get Flanks on data 1” is chosen in the first pull down menu “Fetch sequences…” Then change the second pull down menu (output data type) to “Interval.” FASTA will return a FASTA formatted raw sequence. Interval will return a tab-delineated filewith the sequence, but also the SNP IDs. Click “Execute.”
6. Open the latest dataset “Extract Genomic DNA on data 2” by clicking the linked title. You’ll notice the first three columns are locations, the 4th is SNP ID, the 5th column is unused (0), the 6th column is strand and 7th is the flanking squence. You can nowview the data (click eye icon) or save the tab-delineated textfile to your computer by clicking the “save” link in the dataset description. Save this analysis history as you did in exercise 1.
Your history should look something like this below. You could also import this history (by clicking the green "+") to use in exercise 3: