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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

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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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