To add a new GeneMarkerHTS project
1. On the GeneMarkerHTS main window, click New.
The New Project dialog box opens. If this is the first project that is being run for the GeneMarkerHTS instance, then all the project settings are set to their default values; otherwise, by default, GeneMarkerHTS remembers the settings for the last run project.
2. Optionally, if applicable, to reset all project settings to their default values, click Reset Settings, and then click Yes in the Reset Settings dialog box that opens.
3. Do one of the following to specify the location in which to save the project:
• Leave the Project Folder blank, and then, by default, after you add the project sample files, the project folder is set to the same folder as the project sample files.
• Next to the Project Folder field, click the Browse button to open the Project Save Location dialog box, and then browse to and select where the project (*.pjt) file is to be stored.
• In the Project Folder field, manually enter the full path to the folder in which the project is to be saved.
 | If the specified folder does not exist, then GeneMarkerHTS prompts you to create the path before the project is created. |
4. If the project is to use the default reference that is supplied with GeneMarkerHTS, then select Use Default Reference; otherwise, leave Use Default Reference blank, and then next to the Reference Filename field, click the Browse button to open the Open Reference dialog box, and then browse to and select the reference that the project is to use.
5. If the project is to use the built-in motif that is supplied with GeneMarkerHTS, then leave Use Default Motif selected; otherwise, to use a custom motif, clear Use Default Motif, and the do one of the following:
• To use the default motif as your starting point for creating a custom motif:
a. Clear Use Default Motif.
b. Continue to To create or edit a custom motif.
• To use an existing custom motif as your starting point for creating another custom motif:
a. Clear Use Default Motif.
b. Click the Browse button that is displayed to the right of the Motif Path field, and browse to and select the motif.
c. Continue to To create or edit a custom motif.
6. Specify all the options for the project, including the sequencer. See New Project Dialog Box Settings.
7. To add the samples for the project, click Add to open the Add Samples dialog box, and then select the sample files for the project.
 | After you add at least one sample, you can also right-click any sample and on the context menu that opens, click Add to add another sample. |
The sample files are added to the project and are displayed in the Sample Files pane of the New Project dialog box. The Name for each sample file is automatically generated from the name of the added file.
8. Optionally, you can do any or all of the following for added sample files:
• To change the name of a sample file, double-click the file to select it, and then change the name of the file.
• To remove one or more sample files from a project, select the sample file (CTRL-click to select multiple files), and then click Remove. (You can also right-click any sample file and on the context menu that opens, click Remove.)
• To split paired read sample files into separate sample entries, right-click any one of the paired read sample files, and on the context menu that opens, click Split.
| | To combine split paired read files, right-click any of the paired read sample files, and then on the context menu that opens, click Combine with <filename>. |
• To remove all sample files in a single step, click Remove All.
9. Optionally, do any or all of the following:
• To adjust the settings that affect variant calling and therefore, the variants that are displayed in the Variants table of the Mito Alignment Viewer, click Filter Settings to open the Filter Settings dialog box, and then edit any or all of the values on the Mito Variant tab and/or the Mito Alignment tab.
| | For detailed information about filter settings for an mtDNA alignment project, see Mito Alignment Viewer Filter Settings. |
• To adjust the amplicon regions used for the alignment, click Amplicon Settings, and then add or remove regions as appropriate. See Specifying amplicon regions.
• To adjust the settings that mask the personal health information (PHI) for the subject, click PHI Settings to open the PHI Settings dialog box, and then add and/or remove default and/or custom hidden regions as appropriate. See Masking personal health information (PHI) for a subject.
10. Click OK.
The Project Viewer dialog box opens. The samples that are being processed for the project are displayed on the left side of the dialog box in the form of “Sample buttons.” The progress of processing a sample file is displayed on the right side of the dialog box. After a sample file is successfully processed for a project, the Sample button for the project is enabled. You can click the Sample button for any completed sample file to view its results in either the Mito Alignment Viewer (for an mtDNA only project) or the STR Analysis Viewer (for an STR analysis project), even if other sample files are being processed or are waiting to be processed.
| | Depending on your project setup, other messages might open before the Project Viewer dialog box opens, such as a message about creating a non-existent project folder. Answer all the prompts as needed to resolve any issues and open the Project Viewer dialog box. |
| | For a detailed list of the output files for a GeneMarkerHTS project, see GeneMarkerHTS Project Output Files. |
11. Continue to GeneMarkerHTS Viewers and Reports.