To manually group control sample files
When you group control sample files, each sample control group is considered to be an individual control for training the model. Remember, you must load a minimum of 30 unique control sample files, either individually or as control sample groups. For example, if you load 32 control sample files, and then grouping the files results in 8 control sample groups (4 control sample files per group), then you must load an additional 22 control sample files, or 22 control sample file groups.
1. On the Load Control Samples dialog box, click Group Samples.
The Sample Group Editor dialog box opens.
2. Specify how to group the samples.
Setting | Description |
|---|---|
Group by Sections | Group the sample files based on a user-defined section in the sample file names. The default values for delimiters are a dash (-), a period (.), and an underscore (_). For example, a sample file named F_Sample1_01.fasta would have four sections based on the default underscore and period delimiters: • Section 1 = F • Section 2 = Sample1 • Section 3 = 01 • Section 4 = fasta |
Group by Fixed Position | Group by user-specified position or range of positions in the sample file names. |
Group by Order | Group the jobs based on the order in which the sample files were loaded in to the NextGENe SAD tool. |
 | The last grouping option that was selected remains selected by default when the Group Jobs dialog box opens. |
3. By default, the Group ID for each group is automatically created based on how the samples are grouped. You do have the option of modifying some of the settings that affect how the Group ID is created.
Job Grouping | Default Group Name |
|---|---|
By Sections | The Group ID: section(s) indicates which section of the file name is used to group the sample files. This section is also used for the Group ID. For example, for the following six sample files with the Group ID: section(s) = 1 for grouping: • F_Sample1_01.fasta • D_Sample1_01.fasta • E_Sample1_01.fasta • F_Sample2_02.fasta • D_Sample2_02.fasta • E_Sample2_02.fasta creates three groups with two sample files each and each group identified by one of the following three Group IDs: F, D, or E. |
By Fixed Position | The Group ID is based on the user-specified character (for example, 1) or range of characters (for example, 1-4) in the file names that were used to group the jobs. For example, considering the same sample files above, using Group ID: character(s) = 1 for grouping creates three jobs with two sample files each and each group identified by one of the following three Group IDs: F, D, or E. Note: You can select Match Case to further refine the grouping and the Group IDs. |
By Order | By default, Group ID: the first item name is selected, which means that the ID that is assigned to each job is based on the name of the first file in each group. For example, considering the same sample files above, and using a Group Size = 2, then three groups would be created with two sample files per group and each group identified by one of the following three Group IDs: • F_Sample1_01 • D_Sample1_01 • E_Sample1_01 Note: If you clear <Group ID: the first item name>, then the Group ID is a numeric value and it is created based on the order in which they groups are listed in the Sample Group Editor dialog box (e.g., 1, 2, 3, and so on). |
4. Optionally, build out the sample name by assigning a prefix and/or suffix to the Group ID. For example:
• If the Group ID for three separate groups is “D,” “E,” and “F,” then specifying Sample in the first blank Build Sample Name field results in Group IDs of “SampleD,” “SampleE,” and “SampleF.”
• If you specified another value in the second blank Build Sample Name field (such as the date of the sample run), then the Group IDs would be “SampleD06172018,” “SampleE06172018,” and “SampleF06172018.”
| | To remove the groupings and run the control sample files individually again, you must click Control Samples to open the Load Control Samples dialog box. Click Remove All to remove all control sample files, and then load the sample files again. See Step 2. |
 | After you set up and define a manual sample grouping option, going forward, you can automatically apply this grouping option to all your control sample files. See To automatically group control sample files. |
5. Click OK.
The Group Sample dialog box closes. You return to the Load Control Samples dialog box.
6. Click OK.
The Load Control Samples dialog box closes. You return to the Models page. The control sample files are displayed in their resulting groups in the Samples pane at the bottom of the page.
7. Continue to one of the following: