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Introduction to MiSeqData Analysis and   
BaseSpacegenomics cloud computing
© 2012 Illumina, Inc. All rights reserved.
Illumina, illuminaDx, BaseSpace, BeadArray, BeadXpress, cBot, CSPro, DASL, DesignStudio, Eco, GAIIx, Genetic Energy, Genome Analyzer, GenomeStudio, GoldenGate, HiScan, HiSeq, Infinium, 
iSelect, MiSeq, Nextera, Sentrix, SeqMonitor, Solexa, TruSeq, VeraCode, the pumpkin orange color, and the Genetic Energy streaming bases design are trademarks or registered trademarks of 
Illumina, Inc. All other brands and names contained herein are the property of their respective owners.
Eri Kibukawa
Bioinformatics Support Scientist
APAC Technical Support
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MiSeqReporter
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MiSeqReporter Web-based interface
http://localhost:8042
http://IPaddress:8042
5
eg.  http://192.168.10.16:8042
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Supported Web browser
MSRv2.0 updated the user interface to Silverlight 
to improve performance and support use on a Mac.   
* The UI has been tested on  the following web browsers:
Browser
Version
OS
6
Chrome
20.0
Windows
Firefox
13.0
Windows
IE
IE 8 and IE 9
Windows
Safari
5.1.7 
MacOS!
Applications?
What applications to apply?
DNA
8
RNA
Resequencing
Custom Amplicon
De novo assembly
GenerateFASTQ
LibararyQC
MiSeqReporter Workflows
9
LibararyQC
16S Metagenomics
PCR Amplicon
Small RNA
Standard formatted output files!
FASTQ
BAM
VCF
TXT
HTML
8 Workflows in MiSeqReporter
Library QC
Fast resequencingof a ref genome  to 
QC the DNA library.No variant calling 
Provides per-sample summary statistics.
Custom Amplicon
(TruSeqCustom Amplicon)
Performs alignment and variant calling for a 
TSCA library against it’s manifest file/sequence.
Provides somatic variant caller option.
Resequencing
Performs alignment to a ref genome,
and performs variant calling 
for sequence from a small genome.
PCR Amplicon(
Nextera-fragmented)
Sequencing of Nextera-fragmented PCR 
ampliconsand performs alignment, 
and variant analysisfor ampliconregions.
10
de novo Assembly
Assembles small (<20 Mb) genomes from 
reads.Nogenomic reference needed.
16S Metagenomics
performs 16S rRNAbacterial metagenomic
analysis of a mixed population.
Small RNA 
Provides counts of mature miRNAsequences 
from human.  Adapter sequences
are also masked automatically. 
GenerateFASTQ
Demultiplexand output FASTQ files, 
but perform no other processing.
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