2. Example Amplicon Project Design and Analysis
:
2.2 Project Setup in the AVA Software
: 2.2.7 Importing the Read Data Set
2.2.7
Importing the Read Data Set
The next and final step in the set up of the Project is to add actual read data. This is done using the “Import” button at the left edge of the Project Tab. This button is enabled by selecting either the ‘Read Data’ Tree sub-tab (left panel) or the ‘Read Data’ Definition Table sub-tab (right panel) (
Figure 2‑19
).
Figure 2‑19: The AVA window with both the Read Data Tree and Read Data Definition Table visible. The tree panel was last clicked on, making it the currently “active panel” as indicated by the blue border that surrounds it. The Import button to the left is active and is associated with the type of data in the visible tab of the active panel. In this case, the Import button would allow the import of new Read Data into the project since the tree panel is the “active panel” and the Read Data Tree is selected and visible within it.
Clicking the “Import” button opens the “Choose Read Data” file browser window, which allows us to search for Read Data files to add to the Project. Since the data we want to import resides in a single region of a 4-region sequencing Run (and each region has its own SFF file), we select ‘454 SFF Files’ from the ‘Files of Type:’ drop down menu. We then navigate to the folder that contains the SFF files of the EGFR Run, and select the file that contains the read data we want to import (DGVS90J03.sff). This selection populates the ‘File Name:’ field, in the Choose Read Data window (
Figure 2‑20
).
Figure 2‑20: The Choose Read Data window, with the DGVS90J03.sff file selected
Clicking “OK” opens the Import Read Data window. We choose to use the default ‘Read Group Name’, and to import the data file itself (as opposed to simply creating a symbolic link) (
Figure 2‑21
).
Figure 2‑21: The Import Read Data window, ready to import the file selected
Clicking OK returns us to the AVA window and adds the new Read Data Set to both the Read Data Tree and the Read Data Table (
Figure 2‑22
).
Figure 2‑22: The AVA window, after importing the DGVS90J03.sff Read Data file
Finally, we must associate the Sample-Amplicon groups with the Read Data, so the AVA software can properly demultiplex the reads in the Read Data and assign them to their respective Amplicons. To do this, we select the Read Data Tree and the Samples Definition Table, and drag the Sample_1 to the DGVS90J03 Read Data node. This creates the association between the Sample and the Read Data, with the prior Sample-Amplicon associations also maintained (
Figure 2‑23
). We then click the ‘Save’ button to save all the information we entered, in the Project folder.
Figure 2‑23: The AVA window after creating the association between the Sample_1 and the DGVS90J03 Read Data Set
