To create a new job file in the NextGENe AutoRun tool
1. Do one of the following:
• On the NextGENe main menu, click Tools > NextGENe AutoRun.
• On the Start menu, select All Programs\SoftGenetics\NextGENe\NG_<Version>\NG_AutoRun.
The NextGENe AutoRun window opens.
2. On the NextGENe AutoRun main menu, click Tool > Job Editor.
The Job Editor dialog box opens. It contains a placeholder for creating a job, which is identified with the default name of Job<#>, for example, Job1.
3. For each sample file that is to be analyzed, click Load in the Sample File(s) pane to open a dialog box, and then browse to and select the sample file.
The number of samples that are loaded is displayed above the Input sequence files pane, for example, Input sequence files: 4 files loaded. The job name is automatically updated based on the file name of the first file loaded, but you can modify as needed.
 | You can load multiple samples for analysis with the same job options and then use the Group Jobs option to automatically group samples into separate jobs. The same job options are applied to all the separate job files. See To group jobs in the NextGENe AutoRun tool. |
4. In the Output field, leave the default value for the location of the output files as is (the directory path for the first data file added), or click Set to select a different location.
5. If your project sample files require preprocessing, then you must load the appropriate Settings files (.ini files) to specify the required preprocessing options.
• If the project sample files are not in .fasta or .bam format, then you must load a Settings file that specifies the format conversion settings.
• If the project sample files contain barcodes, then you must load a Settings file that specifies the barcode sorting settings to demultiplex the data.
• If the project sample files need to be modified further before analysis (for example, trimming adapters), then you must load a Settings file that specifies the appropriate sequence operation settings.
If applicable, for any of the above, go to To specify preprocessing options; otherwise, continue to Step 6.
6. In the Reference pane, click the arrow that is next to Select to open a dropdown menu, and then do one of the following:
• To select a preloaded reference, click Select Preloaded Reference to open a Load Reference Files dialog box in which you can select the preloaded reference, and then continue to Step 9.
• To select a GenBank or a .fasta reference file, click Add Sequence Files to open a dialog box in which you can browse to and select the reference file, and then continue to Step 7.
7. If you loaded a GenBank reference file, then “Query annotation and & tracks from preloaded” is displayed below the reference pane with a Select option. If you do not want to query the imported databases (tracks) for the project, then continue to Step 9; otherwise, click Select to open the Select a reference to query annotation and tracks dialog box and select the appropriate preloaded reference.
8. Click OK.
The Select a reference to query annotation and tracks dialog box closes. The Job Editor dialog box remains open.
9. Next to the Process & report settings file field, click Load to open a dialog box, and then browse to and select a configuration file with the appropriately saved settings for the condensation, assembly, and/or alignment steps. (See Saving and Loading Project Settings.)
After you load the Settings file, Report & Export is enabled and the number of
post-processing options that the loaded file contains is displayed. An Edit details link is also enabled.
post-processing options that the loaded file contains is displayed. An Edit details link is also enabled.
10. Optionally, consider the following; otherwise, continue to Step 11.
• If the configuration file that you loaded in Step 9 does not contain post-processing options, and you want to post-process the data:
or
• If the configuration file that you loaded in Step 9 does contain post-processing options, but you want to add more options or use different settings to post-process the data:
then click Edit details to open the Outputs dialog box.
11. Select the appropriate post-processing outputs and the corresponding Settings files (.ini files) by which to post-process the data. See:
12. Click OK on the Outputs dialog box.
The Outputs dialog box closes. The Job Editor dialog box remains opens.
13. Optionally, if either of the following are applicable, then select Inspect input files to set optimum parameters.
• If you loaded a Configuration file that contains condensation settings for Illumina data, SOLiD System data, or Ion Torrent data, and you select this option, then NextGENe inspects the input files and adjusts the condensation settings accordingly. If you select this option for Roche data, then NextGENe simply ignores it.
| | This option is identical to the Inspect Input Files option on the Condensation page in the Project Wizard. See Inspect Input Files. |
• If you loaded a Configuration file that contains alignment settings for a preloaded reference, and you select this option, then NextGENe inspects the input files and adjusts the alignment settings accordingly.
| | This option is identical to the Inspect Input Files option on the Alignment page for preloaded reference files in the Project Wizard. See Inspect Input Files. |
14. If the output is to be exported to Geneticist Assistant, then go to To export the output to Geneticist Assistant; otherwise, continue to Step 15.
15. Optionally, do any of the following as needed; otherwise, continue to Step 16.
• Save the job file.
• Add a new job to the job file.
• Add a secondary analysis job.
• Delete a job.
• Duplicate a job.
• Group samples into jobs.
16. Click OK.
If you have not already clicked Save to save the job file, then you are prompted to specify a file name and location for the job file and after you save the file, the Job Editor dialog box closes; otherwise, the Job Editor dialog box simply closes. You have now created the necessary job files.
17. Continue to To specify the NextGENe AutoRun settings.