Sample and locus management
By doing a right mouse click behind the sample name, you will get a list of options for sample management:
Sample settings:
Here you can indicate what sequencing platform was used.
Set group:
Here you can select 2 options:
'New group': different samples/data files can be combined, e.g. sample /files containing data from different loci from one patient or a patient and its potential donors. The combined group of samples/files can be given a user-defined group name.
'Remove from group': use this option to remove a sample from a group.
Pair: Two files containing paired-end data can be combined and analyzed as if it was one file.
Join: Two data files can be combined to result in a single typing. Use this option for example if sequence data from different exons of the same sample are in separate sequence files.
Unlink: The Pair, Join or Set group options can be undone.
Set display name: A user defined name can be defined for the group or file(s).
Save PDF report:
A complete PDF report will directly be saved for the sample in a "Reports" folder in the Project folder. The file name will be: sample name_date_time_Report.
This PDF report includes the sample summary, detailed loci pages, reads info, analysis settings and reviews table. For more information see the Reports section.
By selecting multiple samples (by using the "Shift" button and clicking on the sample names) and then using the "Save PDF report" option you will get a report for each selected sample.
Add locus:
NGSengine can analyze data files containing data of pooled loci. NGSengine will automatically detect which loci are present in the data file.
However, in some cases, not all loci are recognized. This can happen for example if the DNA concentration of one of the genes was much lower than the other genes. You can add a locus to a data file by using the right mouse button option 'Add locus'. After adding a locus, the sample has to be analyzed again: click on the 'Analyze' button behind the sample name.
If the same locus has to be added to more than one sample, it is advised to first select the samples and then add the locus simultaneously for all selected samples.
Approve / Reject:
Approve or reject all results for this sample. You can also add a comment. For more information on Approval click here.
Comments:
It is also possible to add comments to a sample without approve or reject. When this option is selected, a new window will open. At the bottom part a message/comment can be typed, next click on "Add" to add this comment to the sample. All comments will be shown in the box above, with information about the reviewer and time and date of the comment:
On the Overview screen an icon will be shown behind the sample name to indicate that comments have been added. By hovering with your mouse on the icon, the last comment will be shown:
The sample comments can be added to the PDF report via the Reports settings. For more info click here.
Analyze: start analysis.
Right-mouse click on a locus will open the locus management window:
Locus settings:
This will open the locus settings window, as explained in the part about the Locus settings in the Preferences.
Approve / Reject:
Approve or reject all results for this locus. You can also add a comment. For more information on Approval click here.
Create review copy:
This option can be selected when the locus has been approved by the first reviewer. For more info click here.
Undo approve / reject:
This option can be used to undo the approve or reject for the locus. For more information on Approval click here.
Comments:
It is also possible to add comments to a locus without approve or reject. When this option is selected, a new window will open. At the bottom part a message/comment can be typed, next click on "Add" to add this comment to the sample. All comments will be shown in the box above, with information about the reviewer and time and date of the comment. Also shown is a list of Reviews (approve, reject or reset) with information about the reviewer and time and date of the review. This list of reviews can be removed from the comments by unchecking the "Show reviews" box (see arrow):
On the Overview screen an icon will be shown behind the locus to indicate that comments have been added. By hovering with your mouse on the icon, the last comment will be shown:
The locus comments can be added to the PDF report via the Reports settings. For more info click here.
Analyze: Start analysis.
Remove locus:
The locus will be removed from the sample. After removing a locus, the sample has to be analyzed again: click on the 'Analyze' button behind the sample name.
Prepare submission:
This option can be used to prepare file for the submission of a new allele. For more info click here.