- Welcome
- Introduction
- Publications and presentations
- Signing in
- System requirements
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How To
- Logging into GNomEx
- Submitting an experiment request
- Submitting a microarray hybridization request
- Submitting a sample quality request
- Submitting a sequencing request
- Requesting that microarray hybridization or sequencing be performed on samples previously submitted to sample quality testing
- Adding lanes to a previously submitted sequencing request
- Registering an external experiment in GNomEx
- Finding and viewing a summary of an experiment
- Editing an experiment
- Downloading experiment results
- Linking the samples from an experiment to their BST sample
- Viewing analyses
- Downloading analyzed data files
- Viewing a description of the materials and the methods used during processing of a specific kind of experiment
- Performing a search for experiments and analyses meeting a specific type of criteria
- Submitting a work authorization
- How pricing and billing works in GNomEx
- Adding a new price criterion
- Creating a new price sheet
- Creating a new price category
- Modifying an existing price sheet
- Modifying an existing price category
- Modifying an existing charge item
- Preparing and sending out invoices for clients
- Generating general ledger interface data for automatically billing university accounts
- Window, Tab, and Field Descriptions
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GNomEx Error Messages and Information Windows
- Are you sure you want to delete all the hybridizations?
- Are you sure you want to delete all of the samples?
- At least one non-empty file must be selected in order for download to proceed.
- Please enter all of the required fields for the hybridization.
- Please enter all required fields for the samples.
- Please enter at least one search criterion.
- Please select a price category.
- Please select a price sheet.
- Remove all hybs currently showing in the list?
- Remove all samples currently showing in the list?
- The number of samples to setup has changed. Do you want to clear out the existing samples?
- The request has not been saved. Are you sure you want to quit?
- The request is now assigned to project.
- The webpage you are viewing is trying to close the window.
- Unable to generate GL interface. Cannot find approved folder.
- You are no longer logged on. Please logon again.
- Your changes have not been saved. Are you sure you want to exit?
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Working With the List of Samples Submitting for Microarray Hybridization
- Adding a Sample to the List of Samples You Will Be Submitting for Microarray Hybridization
- Adding a sample to the list of samples you will be submitting for microarray hybridization that is similar to another sample already in the list
- Deleting a sample from the list of samples you will be submitting for microarray hybridization
- Deleting all of the samples currently included in the list of samples you will be submitting for microarray hybridization
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Working With the List of Hybridizations By Requests
- Adding a hybridization to the list of hybridizations you will be requesting
- Adding a hybridization to the list of hybridizations you will be requesting that is similar to another hybridization already in the list
- Deleting a hybridization from the list of hybridizations you will be requesting
- Deleting all of the hybridizations currently included in the list of hybridizations you will be requesting
- Editing a hybridization from the list of hybridizations you will be requesting
- Working with the list of hybridizations you will be requesting
- The hybs tab (submit microarray hybridization request window)
- The submit microarray hybridization request window
- Submitting a microarray hybridization request
- Microarray hybridization requests
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Specialized Role Topics
- Uploading a sample sheet
- Setting/changing the prices of a charge item
- Setting/changing the experiment type(s) associated with a price sheet
- Setting/changing the criteria by which a charge item will be applied to billing for an experiment
- The sample view tab (new experiment module)
- The hyb setup tab (new experiment request module)
- The hyb view tab (new experiment request module)
- The new project window
- The edit project window
- Adding a new project while you are entering a microarray hybridization request
- Editing an existing project while entering a microarray hybridization request
- Adding a new sample characteristic for annotation while submitting a sample hybridization
- Editing an existing sample characteristic for annotation while submitting a sample hybridization
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Guides
- User Guide
- Experiment orders
- The foundation of GNomEx
- Experiments at a glance
- Submitting a HiSeq or MiSeq experiment order
- ABI Capillary (Sanger) Sequencing
- Checking on experiment progress
- Copy and pasting into samples grid
- Posting outside experiment data
- iScan experiments
- Downloading and uploading your data
- The download files window
- Downloading large data sets
- Downloading chromatograms
- Fast data transfer from the command line
- Troubleshooting guide for downloading
- Launching FDT with Webstart
- Uploading your data
- Annotating your experiment
- Associating experiment files back to the samples
- Sample annotations
- Copy and paste for the samples grid
- Bulk sample sheet import
- Analysis and data tracks
- Create an analysis
- Data tracks
- Disk usage
- Configuring GNomEx
- Context-sensitive help
- Customize the billing account fields
- Dictionaries
- Seq lib protocols and barcode schemes
- Configuring HiSeq rapid mode sequencing options
- Developer Guide
- Installation Guide
- Configuring GNomEx for FDT
- Configuring GNomEx to use LDAP Authentication
- Compiling and Building
- The Database Schema
- GNomEx Open Source
- Developer Documents
- Illumina HiSeq Realtime Info — The Metrix Server
- FAQs
- Demo
To download analyzed data files:
1. Start the Analysis module by clicking on the large Download Analyzed data files button in the Analysis section of the home page of the application environment.
2. Find the appropriate analysis in the list of analyses in the module — see Viewing Analyses for more details about how to go about doing this in the Analysis module. Click on that analysis in the list. The analysis summary will appear on the right side of the window.
3. Click on the Files tab on the analysis summary page.
A list of downloadable files that are associated with the analysis will appear.
4. Select the files you wish to download by checking the box on the left side of each applicable row in the files list.
You can also select an entire set of files associated with an analysis. In order to do this, rather than selecting a specific analysis in the analysis list, select the lab that submitted the analysis. Then, select the Downloads tab in the area on the right side of the window. A list of analyses with associated downloadable files will appear. Select the appropriate analysis by clicking on its checkbox.
5. Click on the Download button in the lower part of the screen (beneath the files list).
GNomEx will estimate how much data you are about to download. It does this to give you an idea of how much time it might take to download the indicated materials. This estimate is displayed and you are asked if you would like to continue with the download. (Click No if you want to abort the download at this point).
6. Click Yes to confirm that you want to proceed with the download. A typical Save As dialog will appear so that you can choose a location to store the downloaded files.
7. Choose a location to store the downloaded information on your computer hard drive or a network volume as appropriate and click Save to initiate the download to that location.
The files will be downloaded in a .zip file. You may need to extract the files from this compressed folder using a zip file extraction application in order to view them properly.
