20130702 set up_miseq_generead_dn_aseq_gene_panel

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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


Sample & Assay Technologies Check Software Version of the Experiment Manger


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)


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


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


Sample & Assay Technologies Create a Sample Sheet


Click „Folder Settings“

Double Click .

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Check Directories. Defaults are:



Click „Create Sample Sheet“

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Click „MiSeq“ � „Next“



Click „Other“ � „FASTQ Only“ � „Next“

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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“



Check „Maximize“

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Press „Add Blank Row“ – one Click per Sample/Library – each Click adds a row



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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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).



Follow Instructions in MiSeq™ Reagent Kit Reagent Preparation Guide

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Follow Instructions in MiSeq™ Reagent Kit Reagent Preparation Guide



Follow Instructions in MiSeq® System User Guide

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Follow the Instructions of the Wizard in the MiSeq Control Software

Click „Sequence“



Uncheck „Use Base Space....“ � Click „Next“

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Follow the Instructions on the screen to load a flowcell, cartridge and buffer...



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Sample & Assay Technologies 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

20130702 set up_miseq_generead_dn_aseq_gene_panel

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