1. 07.02.2013
Sample & Assay Technologies
Setting up MiSeq to run GeneRead DNAseq Gene
Panel Libraries
02-07-2013
Sample & Assay Technologies
Holger Wedler
Check Software Version of the MiSeq Control Software
Get sure to have installed MiSeq Control Software 2.0.5.0 or later:
After booting of the MiSeq, usually the MiSeq Control Software is
launched automatically.
Otherwise double click symbol
on the desktop.
Click to get details
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2. 07.02.2013
Sample & Assay Technologies
Check Software Version of the MiSeq Control Software
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Sample & Assay Technologies
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Check Software Version of the Experiment Manger
Get sure to have installed Experiment Manager Software 1.3 or
later:
Double click symbol
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on the desktop.
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3. 07.02.2013
Sample & Assay Technologies
Check Software Version of the Sequencing Analysis Viewer
(SAV)
Get sure to have installed Sequencing Analysis Software 1.8.11 or
later:
Double click symbol
on the desktop.
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Sample & Assay Technologies
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Check Software Version of the MiSeq Reporter
Get sure to have access to installed MiSeq Reporter Software
2.0.26 or later via Internet Browser:
Enter address „http://XX.XXX.XX.XX:XXXX/default.htm“ or
http://127.0.0.1:8042 in the Internet Explorer of the MiSeq.
Ask your IT specialists and/ Illumina support for details.
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4. 07.02.2013
How to Start a Run
Sample & Assay Technologies
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Create a Sample Sheet
Sample & Assay Technologies
Click „Folder Settings“
Double Click
.
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5. 07.02.2013
Sample & Assay Technologies
Create a Sample Sheet
Check Directories. Defaults are:
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Sample & Assay Technologies
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Create a Sample Sheet
Click „Create Sample Sheet“
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6. 07.02.2013
Sample & Assay Technologies
Create a Sample Sheet
Click „MiSeq“
„Next“
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Sample & Assay Technologies
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Create a Sample Sheet
Click „Other“
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„FASTQ Only“
„Next“
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7. 07.02.2013
Sample & Assay Technologies
Create a Sample Sheet
Enter „Reagent Cartridge Barcode“ (required)
select „TruSeq
LT“
Select „Index Reads 1“
Select „Read Type Paired End“
Enter „Cycles Read 1: 151“, „Cycles Read 2: 151“
Check „Use
Adapter Trimming“
All other fields are optionally, but useful.
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Sample & Assay Technologies
Click „Next“
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Create a Sample Sheet
Check „Maximize“
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8. 07.02.2013
Sample & Assay Technologies
Create a Sample Sheet
Press „Add Blank Row“ – one Click per Sample/Library – each
Click adds a row
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Sample & Assay Technologies
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Create a Sample Sheet
In this example 5 rows were added. Entering „Sample ID“ and
selection of „Index 1 (I7) is mandatory, all other fields are optionally
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9. 07.02.2013
Sample & Assay Technologies
Create a Sample Sheet
Example:
This Warning
can be ignored
(it seems to be a bug)
Click „Finish“ to save the Sample Sheet in *csv format (s. Folder Settings).
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Sample & Assay Technologies
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How to Start a Run
Follow Instructions in MiSeq™ Reagent Kit Reagent Preparation Guide
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10. 07.02.2013
Sample & Assay Technologies
How to Start a Run
Follow Instructions in MiSeq™ Reagent Kit Reagent Preparation Guide
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Sample & Assay Technologies
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How to Start a Run
Follow Instructions in MiSeq® System User Guide
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11. 07.02.2013
Sample & Assay Technologies
How to Start a Run
Follow the Instructions of the Wizard in the MiSeq Control Software
Click „Sequence“
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Sample & Assay Technologies
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How to Start a Run
Uncheck „Use Base Space....“
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Click „Next“
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12. 07.02.2013
Sample & Assay Technologies
How to Start a Run
Follow the Instructions on the screen to load a flowcell, cartridge
and buffer...
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Sample & Assay Technologies
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13. 07.02.2013
Sample & Assay Technologies
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Sample & Assay Technologies
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14. 07.02.2013
Sample & Assay Technologies
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Sample & Assay Technologies
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15. 07.02.2013
Sample & Assay Technologies
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Sample & Assay Technologies
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FASTQ Files
After the run, data analysis (generation of FASTQ files including
demultiplexing) is done automatically.
FASTQ files are zipped and stored in directory
D:/MiSeqAnalysis/<RunFolder>/Data/Intensities/BaseCalls
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