Sample annotations can be entered or updated at any time. Most frequently, annotations will be uploaded at the time an experiment is created. However, GNomEx also allows for additional annotations to be added to existing experiments, and for existing annotations to be edited or updated.

Entering sample annotations for a small number of samples

1. Create Project and Experiment , or select an existing Experiment

2. In the Experiment window, click on the Edit link. NOTE: The Edit link will only be visible for Experiments for which you have editing privileges. The Owner, Lab PI, and Admin group all have editing privileges."][/tagline_box]

3. Click on the Annotations tab, and check the boxes for all applicable annotations. All 'required' annotations will already be checked.

4. Click on the Samples tab. You will see empty fields highlighted in yellow. Click a cell and enter the appropriate information for that sample annotation. Enter information for all samples and all fields for which you have annotation data. You do not need to enter information into every cell.

5. Additional samples can be entered by right-clicking and selected the 'Add Sample' menu. There is also a menu option to 'Duplicate Sample'.

6. Click Next

7. Review entered data. If everything is correct, press the Save button.

Updating existing annotations using the Download Sample Sheet.

This upload function works on an experiment level. If you want to update sample annotations across multiple experiments, you can use the Bulk Sample Sheet Import.

The steps below show how to update a single annotation for a group of samples. For example, if a gene is discovered after sequencing files are uploaded, then the annotation called Allele Name will need to be updated to correspond with the Gene Name, and the Gene Name will need to be added.

1. Select an existing Experiment, click Edit, and go to the Samples tab.

2. Click on the 'Download Sample Sheet' link. Save the .txt file.

3. Open the .txt Sample Sheet file in Excel. Make your changes to the spreadsheet and save. There will be many columns that don't apply. Save your .txt file in Excel. (You must keep it in this format for the upload to work).

4. Now click on the 'Upload Sample Sheet' link. Select the file you just modified.

5. Only pick the annotations you intend on updating. For the most part, the wizard should do this for you by only selecting the columns that have data filled in.

Figuring out which Required Annotations are Missing

To get a report showing how completely the annotations are filled in for each lab's experiments, run Reports -> Annotation Progress Report.

This will generate an Excel spreadsheet that provides three worksheets. The first sheet shows the experiments missing 'required' sample annotations. The cells marked in red denote missing annotations.

The last column indicates if experiment files are associated back to the appropriate samples. If this column is marked red, you will need to associate the experiment files back to the samples using this from the 'Manage Files' window. This feature is described here: Associating Experiment Files back to the Samples.

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