20130702 set up_miseq_generead_dn_aseq_gene_panel
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07.02.2013
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Sample & Assay Technologies
Setting up MiSeq to run GeneRead DNAseq Gene
Panel Libraries
Holger Wedler02-07-2013
Sample & Assay Technologies Check Software Version of the MiSeq Control Software
Title, Location, Date 2
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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Sample & Assay Technologies Check Software Version of the MiSeq Control Software
Title, Location, Date 3
Sample & Assay Technologies Check Software Version of the Experiment Manger
Title, Location, Date 4
Get sure to have installed Experiment Manager Software 1.3 or later:
Double click symbol on the desktop.
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Sample & Assay TechnologiesCheck Software Version of the Sequencing Analysis Viewer (SAV)
Title, Location, Date 5
Get sure to have installed Sequencing Analysis Software 1.8.11 or later:
Double click symbol on the desktop.
Sample & Assay Technologies Check Software Version of the MiSeq Reporter
Title, Location, Date 6
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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Sample & Assay Technologies How to Start a Run
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Sample & Assay Technologies Create a Sample Sheet
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Click „Folder Settings“
Double Click .
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Sample & Assay Technologies Create a Sample Sheet
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Check Directories. Defaults are:
Sample & Assay Technologies Create a Sample Sheet
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Click „Create Sample Sheet“
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Sample & Assay Technologies Create a Sample Sheet
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Click „MiSeq“ � „Next“
Sample & Assay Technologies Create a Sample Sheet
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Click „Other“ � „FASTQ Only“ � „Next“
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Sample & Assay Technologies Create a Sample Sheet
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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. � Click „Next“
Sample & Assay Technologies Create a Sample Sheet
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Check „Maximize“
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Sample & Assay Technologies Create a Sample Sheet
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Press „Add Blank Row“ – one Click per Sample/Library – each Click adds a row
Sample & Assay Technologies Create a Sample Sheet
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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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Sample & Assay Technologies Create a Sample Sheet
Title, Location, Date 17
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).
Sample & Assay Technologies How to Start a Run
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Follow Instructions in MiSeq™ Reagent Kit Reagent Preparation Guide
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Sample & Assay Technologies How to Start a Run
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Follow Instructions in MiSeq™ Reagent Kit Reagent Preparation Guide
Sample & Assay Technologies How to Start a Run
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Follow Instructions in MiSeq® System User Guide
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Sample & Assay Technologies How to Start a Run
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Follow the Instructions of the Wizard in the MiSeq Control Software
Click „Sequence“
Sample & Assay Technologies How to Start a Run
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Uncheck „Use Base Space....“ � Click „Next“
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Sample & Assay Technologies How to Start a Run
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Follow the Instructions on the screen to load a flowcell, cartridge and buffer...
Sample & Assay Technologies
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Sample & Assay Technologies
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Sample & Assay Technologies
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Sample & Assay Technologies
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Sample & Assay Technologies
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Sample & Assay Technologies
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Sample & Assay Technologies FASTQ Files
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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