How to set up a SamplePrepKit file
IEM stores barcode sets as text files with a specific format. These barcode sets are then plugged into the various Applications listed in IEM. These barcode sets are labeled as SamplePrepKits.
Bioo Scientific has already generated the appropriate data files for the following NEXTflex Kits, which can be downloaded from the table below.
To install the above SamplePrepKit files, first locate the installation path for IEM. The default installation at time of writing on Windows 7 is:
C:\Program Files (x86)\Illumina\Illumina Experiment Manager
Within the Illumina Experiment Manager folder, navigate to the SamplePrepKits folder. Inside this folder are a number of pre-installed Illumina barcode sets.
Copy the appropriate downloaded NEXTflex Barcodes.txt file into the SamplePrepKits directory. The barcode set is now placed so IEM can read its contents.
Plug-in the NEXTflex Barcode sets into IEM Applications
IEM requires that barcode sets are registered with each applicable application. Navigate back to the main directory and open the Applications folder. This folder should have a similar path to the below:
C:\Program Files (x86)\Illumina\Illumina Experiment Manager\Applications
The applications folder features separate sequencing build text files that provide specific settings. Amplicon pools may be handled differently from Resequencing, for example.
To incorporate the Bioo Scientific NEXTflex Barcode sets into a specific application, open the chosen application text file using a text editor such as Notepad on Windows. You may need to open Notepad or other editors as Administrator in Windows 7 as IEM places write protections on its files.
For example, I want to update ChIP-Seq.txt with Bioo Scientific’s 6nt Barcodes. The file appears in Notepad below:
To add the Bioo Scientific 6nt barcode set to the ChIP-Seq application, find the
[Compatible Sample Prep Kits]
line and paste the following underneath (in addition to other Sample Prep Kits mentioned):
Bioo NEXTflex 6nt Barcodes
(For the 8nt Barcodes, paste Bioo NEXTflex 8nt Barcodes)
Below is the file after editing:
Save the file. If Notepad displays an Access Denied warning, reopen Notepad under Administrator mode and repeat the preceding steps.
Open IEM and Create a Sample Sheet
Now that the NEXTflex Barcode indices are properly set up, proceed with generating a new sample sheet for the next sequencing run as usual. When the Workflow Parameter screen appears, the Bioo NEXTflex adapters will be selectable in the barcode set dropdown menu:
Moving to the Sample Selection spreadsheet, the Index1 (I7) column displays B001 through B048 (C001 to C096 for the 8 nt Barcode set), which correspond to Barcodes 1 to 48 of the NEXTflex 6 nt Barcode kits. At this point, the proper barcode indices have been implemented in IEM and are ready for repeated use. For generating a sample sheet with more than 96 samples, see our guide How to Easily Generate Sample Sheets with More than 96 Samples in Illumina Experiment Manager.
If you have any questions, please contact Bioo Scientific at 1-888-208-2246, 1-512-707-8993 or by email at Bioo.NGS@PerkinElmer.com.