07.02.2013

Sample & Assay Technologies

Setting up MiSeq to run GeneRead DNAseq Gene
Panel Libraries
02-07-2013

Sample &...
07.02.2013

Sample & Assay Technologies

Check Software Version of the MiSeq Control Software

Title, Location, Date

Samp...
07.02.2013

Sample & Assay Technologies

Check Software Version of the Sequencing Analysis Viewer
(SAV)
Get sure to have i...
07.02.2013

How to Start a Run

Sample & Assay Technologies

Title, Location, Date

7

Create a Sample Sheet

Sample & Ass...
07.02.2013

Sample & Assay Technologies

Create a Sample Sheet
Check Directories. Defaults are:

Title, Location, Date

Sa...
07.02.2013

Sample & Assay Technologies

Create a Sample Sheet
Click „MiSeq“

„Next“

Title, Location, Date

Sample & Assa...
07.02.2013

Sample & Assay Technologies

Create a Sample Sheet
Enter „Reagent Cartridge Barcode“ (required)
select „TruSeq...
07.02.2013

Sample & Assay Technologies

Create a Sample Sheet
Press „Add Blank Row“ – one Click per Sample/Library – each...
07.02.2013

Sample & Assay Technologies

Create a Sample Sheet
Example:

This Warning
can be ignored
(it seems to be a bug...
07.02.2013

Sample & Assay Technologies

How to Start a Run

Follow Instructions in MiSeq™ Reagent Kit Reagent Preparation...
07.02.2013

Sample & Assay Technologies

How to Start a Run
Follow the Instructions of the Wizard in the MiSeq Control Sof...
07.02.2013

Sample & Assay Technologies

How to Start a Run
Follow the Instructions on the screen to load a flowcell, cart...
07.02.2013

Sample & Assay Technologies

Title, Location, Date

25

Title, Location, Date

26

Sample & Assay Technologies...
07.02.2013

Sample & Assay Technologies

Title, Location, Date

27

Title, Location, Date

28

Sample & Assay Technologies...
07.02.2013

Sample & Assay Technologies

Title, Location, Date

Sample & Assay Technologies

29

FASTQ Files
After the run...
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20130702 set up_miseq_generead_dn_aseq_gene_panel

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20130702 set up_miseq_generead_dn_aseq_gene_panel

  1. 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 Title, Location, Date 2 1
  2. 2. 07.02.2013 Sample & Assay Technologies Check Software Version of the MiSeq Control Software Title, Location, Date Sample & Assay Technologies 3 Check Software Version of the Experiment Manger Get sure to have installed Experiment Manager Software 1.3 or later: Double click symbol Title, Location, Date on the desktop. 4 2
  3. 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. Title, Location, Date Sample & Assay Technologies 5 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. Title, Location, Date 6 3
  4. 4. 07.02.2013 How to Start a Run Sample & Assay Technologies Title, Location, Date 7 Create a Sample Sheet Sample & Assay Technologies Click „Folder Settings“ Double Click . Title, Location, Date 8 4
  5. 5. 07.02.2013 Sample & Assay Technologies Create a Sample Sheet Check Directories. Defaults are: Title, Location, Date Sample & Assay Technologies 9 Create a Sample Sheet Click „Create Sample Sheet“ Title, Location, Date 10 5
  6. 6. 07.02.2013 Sample & Assay Technologies Create a Sample Sheet Click „MiSeq“ „Next“ Title, Location, Date Sample & Assay Technologies 11 Create a Sample Sheet Click „Other“ Title, Location, Date „FASTQ Only“ „Next“ 12 6
  7. 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. Title, Location, Date Sample & Assay Technologies Click „Next“ 13 Create a Sample Sheet Check „Maximize“ Title, Location, Date 14 7
  8. 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 Title, Location, Date Sample & Assay Technologies 15 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 Title, Location, Date 16 8
  9. 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). Title, Location, Date Sample & Assay Technologies 17 How to Start a Run Follow Instructions in MiSeq™ Reagent Kit Reagent Preparation Guide Title, Location, Date 18 9
  10. 10. 07.02.2013 Sample & Assay Technologies How to Start a Run Follow Instructions in MiSeq™ Reagent Kit Reagent Preparation Guide Title, Location, Date Sample & Assay Technologies 19 How to Start a Run Follow Instructions in MiSeq® System User Guide Title, Location, Date 20 10
  11. 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“ Title, Location, Date Sample & Assay Technologies 21 How to Start a Run Uncheck „Use Base Space....“ Title, Location, Date Click „Next“ 22 11
  12. 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... Title, Location, Date 23 Title, Location, Date 24 Sample & Assay Technologies 12
  13. 13. 07.02.2013 Sample & Assay Technologies Title, Location, Date 25 Title, Location, Date 26 Sample & Assay Technologies 13
  14. 14. 07.02.2013 Sample & Assay Technologies Title, Location, Date 27 Title, Location, Date 28 Sample & Assay Technologies 14
  15. 15. 07.02.2013 Sample & Assay Technologies Title, Location, Date Sample & Assay Technologies 29 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 Title, Location, Date 30 15

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