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Discussion:
This procedure describes how to Create a Gel/Plate Sample Sheet and Pre-process the sequencer Run Folder
in preparation for Process the Run Folder into dnaLIMS. This procedure is a multi-step process.
Overview Steps:
1. Sequencing Requests are selected from the sequencing queue and ordered into a Sample Sheet.
This Gel Sample Sheet is assigned a numeric name. An example would be Gel or Sample Sheet 460.
2. The Sample Sheet is copied across the network to the computer controlling the sequencer.
The Data Collection program is launched and the Sample Sheet is imported.
3. The sequencer is run. The sequencer resuls are stored in a Run Folder.
4. The Run Folder is copied across the network into the TO-UNIX directory of dnaLIMS.
5. The Run Folder name is associated with the Sample Sheet Number within dnaLIMS.
6. The sequencer reaction results are entered into dnaLIMS.
7. The Run Folder is Processed into dnaLIMS (See procedure Process Run Folder into dnaLIMS.)
Use the following forms to Create a Sample Sheet:
1. View Sequencing Requests
2. Recycle/Delete Sample Sheet/Samples
3. Create Sequencer Sample Sheet
Use the following form to copy the Sample Sheet across the network:
1. View Sample Sheets & Reaction Sheets
Use the following forms to Pre-process a Run Folder:
1. Enter Run Folder Name
2. Enter Sequencing Results
Use the following form to Process a Run Folder into dnaLIMS:
1. Process Run Folder into dnaLIMS
2. Delete Run Folder in TO-UNIX
Overview:
The Create Sequencer Sample Sheet form is used to assign Sequencing Requests to a Sample Sheet.
The samples are processed through the sequencer with the resulting sequence and trace files being located
within a Run Folder. The sequencing results are observed with the success or failure of the reactions
being noted. The contents of the Run Folder are rearranged so that the top level Run Folder contains the
sequencing results and any extraneous Run Folders and sequencer files are deleted. dnaLIMS does not process
embedded Run Folders.
After the Run Folder contents are rearranged, use a FTP program like Fetch or cuteFTP, to copy the Run Folder
across the network to the TO-UNIX directory within the dnaLIMS computer.
This step is mandatory.
Once the Run Folder is copied to the dnaLIMS computer, the Run Folder Name is assigned to its
asociated Sample Sheet Number.
The Run Folder is typically renamed to include the sample sheet number in the name. Example: rf460
This step is mandatory.
The success or failure of each sample reaction is entered into dnaLIMS Results Database.
dnaLIMS cannot process a Run Folder into dnaLIMS before the Results Database is updated.
The Process Run Folder into dnaLIMS form is used to process the Run Folder into the dnaLIMS.
During this processing step, the system manager can select multiple processing options. For example,
the sequence and trace files can be emailed to the user. Local nucleotide libraries can be created
with the sequences. The sequences can be blast searched against local nucleotide libraries.
After the Run Folder is processed into the dnaLIMS successfully, the Run Folder directory within
TO-UNIX can be deleted.
This completes the overview.
The following procedure is a step-by-step guide to creating and processing Sample Sheets.
This procedure references a Sample Sheet created on an ABI377 sequencer.
This same process applies to Sample Sheets created for other sequencers.
Procedure:
A. Create a Sample Sheet
1. Select the View Sequencing Requests hyperlink to view the sequencing pool and verify
sequencing requests are available for processing.
Return to the dnaLIMS home page.
2. Select the Recycle/Delete Sample Sheet/Samples hyperlink to recycle any
out-of-pool sequencing requests. Select the
Recycle All radio button then the Submit button.
Return to the dnaLIMS home page.
3. Select the Create Sequencer Sample Sheet hyperlink to create a Sample Sheet.
4. Select the Sequencer Type and the Comb or Well Plate size.
5. If Necessary, change the sort select list to display the desired sort or no sort at all,
then select the Submit button.
The Load Plate form is displayed.
6. Select the Auto Load Well Plate button and observe the samples populate the Well Plate.
7. Select the Submit button. This will automatically create the Sample Sheet with the selected samples
and display the number naming the Sample Sheet. Remember the Sample Sheet Number.
8. Return to dnaLIMS home page.
9. Select the View Sample Sheets & Reaction Sheets hyperlink.
10. Select the Sample sheet number from step 7 above.
Select the View Sample Sheet radio button and select the Submit button.
The Sample Sheet table is displayed along with the FTP Sample Sheet hyperlink.
11. Select the FTP Sample Sheet hyperlink.
This will initiate a FTP download of the Sample Sheet Spreadsheet file.
This will save the Sample Sheet spreadsheet in a tab delimited file on your computer.
This file can be Imported into the Data Collection Unit.
Process the Sample Sheet and review the results.
B. Transfer the Run Folder to the TO-UNIX directory of the UNIX computer.
dnaLIMS does not process embeded Run Folders.
Rename the Run Folder as in the following example: rf460
1. The sequencer creates a top level Run Folder which contains the Run, Log, Gel, and another
embedded Run Folder that contains the Sequence and Trace files.
If it is desired to have the Run, Log, and Gel files archived on the UNIX computer, rearrange the
contents of the Run Folder so there are no embeded directories. Either click and drag the Run,
Log, and Gel files into the embedded Run Folder, or copy the sequence and trace files up to the
top level Run Folder. Then delete the embedded Run Folder.
If the Run, Log, and Gel files will not be archived on the UNIX computer, select the embeded
Run Folder when transfering the Run Folder, described below.
2. Using a FTP program, like Fetch, Copy the Run Folder across the network to the TO-UNIX directory
on the dnaLIMS computer.
C. Enter Run Folder Name.
1. Select the Enter Run Folder Name hyperlink to assign the Run Folder Name to its
associated Sample Sheet Number.
2. Select the Sample Sheet Number from the Sample Sheet Number select list.
3. Select the associated Run Folder from the TO-UNIX Run Folder select list.
4. Select the Submit Button, and return to dnaLIMS home page.
D1. Enter Sequencing Results.
1. Select the Enter Sequencing Results hyperlink to update the database regarding the success
or failure of each sample. Enter the Sample Sheet number to display the appropriate Sample Sheet.
Select the Submit button.
2. A sequencing results chart will be displayed.
Select the checkboxes that correspond to samples that failed.
Select the Submit button on the chart.
3. If some samples were checked as failed, these samples are displayed in a separate table.
This table includes checkboxes to Rerun the samples.
4. Select the Rerun checkboxes to return the sample to the sequencing pool for reprocessing
in a different Sample Sheet.
5. Return to dnaLIMS home page.
D2. Process the Run Folder into dnaLIMS.
The Run Folder is Processed into dnaLIMS with Process Run Folder into dnaLIMS.
D3. Delete the Run Folder.
1. Select the Delete Run Folder hyperlink.
2. Select the Run Folder to delete from the select list.
Select the Submit button.
3. Return to the dnaLIMS home page.
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