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RNA-seq Analysis Portal
USER MANUAL
Manual for
QIAGEN RNA-seq Analysis Portal 3.0.1
October 28, 2022 This software is for research purposes only.
QIAGEN Aarhus Silkeborgvej 2 Prismet DK-8000 Aarhus C Denmark
QIAGEN RNA-seq Analysis Portal 3.0.1 User Manual
2
Contents
Introduction
6
General information . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6
Intended use statement . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6
General Description
7
Deployment . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7
Supported sample kits . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7
Accessing RNA-seq Analysis Portal . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9
Analysis credits for RNA-seq Analysis Portal . . . . . . . . . . . . . . . . . . . . . . . . 9
Getting Started
11
Upload sequencing data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11
Align and count . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13
Create experiment . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16
View and filter results . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19
What's next - sending results to GeneGlobe . . . . . . . . . . . . . . . . . . . . . . . . 20
Next steps in GeneGlobe . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20
User Interface
23
RNA-seq Analysis Portal terminology and data organization . . . . . . . . . . . . . . . . 24
Analysis Portal page . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25
QIAGEN RNA-seq Analysis Portal 3.0.1 User Manual
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Samples page . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29
Starting Analysis
33
Align and count dialog . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33
Create experiment dialog . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 34
Compare analyses dialog . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 38
Viewing Results
40
Experiment summary and QC report . . . . . . . . . . . . . . . . . . . . . . . . . . . . 40
Differential expression view . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 44
Comparison view . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 52
RNA-seq Analysis Portal analysis explained
53
Align and count analysis workflows . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 53
Create experiment analysis workflow . . . . . . . . . . . . . . . . . . . . . . . . . . . . 58
Taxonomic profiling of unmapped reads . . . . . . . . . . . . . . . . . . . . . . . . . . 59
Compare analyses . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 60
Appendix A - Sequence file naming pattern
61
Appendix B - Reference and annotation information
63
General references and annotations . . . . . . . . . . . . . . . . . . . . . . . . . . . . 63
Sample kit specific resources . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 70
Appendix C - Analysis workflow versions, species support and parameters
72
QIAseq miRNA Library Kit . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 75
QIAseq UPX 3' Transcriptome Kit . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 78
QIAseq UPXome RNA Lib Kit . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 81
QIAseq UPXome RNA Lib Kit (N6-T RT primer) . . . . . . . . . . . . . . . . . . . . . . . 83
QIAseq UPXome RNA Lib Kit (ODT-T RT primer) . . . . . . . . . . . . . . . . . . . . . . 85
QIAGEN RNA-seq Analysis Portal 3.0.1 User Manual
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QIAseq UPXome RNA Lib Kit (N6-T + ODT-T RT primers) . . . . . . . . . . . . . . . . . . 87 QIAseq Stranded mRNA Select/Stranded Total RNA Lib Kit . . . . . . . . . . . . . . . . 90 TruSeq Stranded Total RNA Library Prep (Human/Rat, Gold, Globin) . . . . . . . . . . . 92 Illumina Stranded Total RNA Prep with Ribo-Zero Plus . . . . . . . . . . . . . . . . . . . 94 NEBNext Ultra II Directional RNA Library Prep Kit for Illumina . . . . . . . . . . . . . . . 96 KAPA RNA HyperPrep Kit . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 98 SMARTer Stranded Total RNA Sample Prep Kit - HI Mammalian/Low Input Mammalian . 100 Collibri Stranded RNA Library Prep Kit for Illumina Systems . . . . . . . . . . . . . . . . 102
QIAGEN RNA-seq Analysis Portal 3.0.1 User Manual
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