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• Introduction
• General Description
  • Supported sample kits and sequencing platforms
  • Accessing RNA-seq Analysis Portal
  • Analysis credits for RNA-seq Analysis Portal
• Getting Started
  • Upload sequencing data
  • Align and count
  • Create experiment
  • View and filter results
  • What's next - send results downstream
  • Design follow-up experiments in GeneGlobe
• User Interface
  • Analysis Portal page
    • Front page and Projects overview
    • Project view
    • Send copy of project
  • Samples page
• Starting Analyses
  • Align and count dialog
    • QIAseq UPX 3' Transcriptome Kit and QIAseq UPXome RNA Lib Kit specific settings
  • Create experiment dialog
    • Sample grouping
    • Experimental design
  • Compare analyses dialog
• Viewing Results
  • Experiment summary and QC report
  • Differential expression view
    • Feature table
    • Volcano plot
    • Heat map
    • Biological insights table
    • Filter
    • Send results to GeneGlobe
    • Send results to QIAGEN IPA
  • Comparison view
• RNA-seq Analysis Portal analysis explained
  • Align and count analysis workflows
    • Align and count - QIAseq miRNA Library Kit
    • Align and count - QIAseq UPX 3' Transcriptome Kit
    • Align and count - QIAseq UPXome RNA Lib Kit
    • Align and count - Demultiplexed RNA sample kits
  • Create experiment analysis workflow
  • Taxonomic profiling of unmapped reads
  • Compare analyses
• Appendix A - Sequence file naming pattern
• Appendix B - Reference and annotation information
  • General references and annotations
  • Sample kit specific resources
• Appendix C - Analysis workflow versions, species support and parameters
  • QIAseq miRNA Library Kit (Illumina)
  • QIAseq miRNA Library Kit (Thermo Fisher)
  • QIAseq UPX 3' Transcriptome Kit
  • QIAseq UPXome RNA Lib Kit
  • QIAseq UPXome RNA Lib Kit (N6-T RT primer)
  • QIAseq UPXome RNA Lib Kit (ODT-T RT primer)
  • QIAseq UPXome RNA Lib Kit (N6-T + ODT-T RT primers)
  • QIAseq FastSelect RNA Lib Kit (N6-T RT primer)
  • QIAseq FastSelect RNA Lib Kit (ODT-T RT primer)
  • QIAseq FastSelect RNA Lib Kit (N6-T + ODT-T RT primers)
  • QIAseq Stranded mRNA Select/Stranded Total RNA Lib Kit
  • TruSeq Stranded Total RNA Library Prep (Human/Rat, Gold, Globin)
  • Illumina Stranded Total RNA Prep with Ribo-Zero Plus
  • NEBNext Ultra II Directional RNA Library Prep Kit for Illumina
  • KAPA RNA HyperPrep Kit
  • SMARTer Stranded Total RNA Sample Prep Kit - HI Mammalian/Low Input Mammalian
  • Collibri Stranded RNA Library Prep Kit for Illumina Systems
• Appendix D - RNA-seq Analysis Portal for QIAGEN IPA users
• Appendix E - Quality control details
  • QIAseq miRNA Library Kits
  • QIAseq UPX 3' Transcriptome Kits
  • QIAseq Stranded RNA Library Kits (FastSelect RNA Library Kit, Stranded mRNA/Stranded Total RNA Library Kits), QIAseq UPXome Kit, and all third-party kits

Supported sample kits and sequencing platforms

RNA-seq Analysis Portalsupports analysis of FASTQ data generated on Illumina^® instruments using the following sample kits:

QIAGEN

• QIAseq^® Stranded mRNA Select Kit
• QIAseq^® Stranded Total RNA Lib Kit
• QIAseq^® miRNA Library Kit
• QIAseq^® UPX 3' Transcriptome Kit
• QIAseq^® FastSelect RNA Lib Kit
• QIAseq^® UPXome RNA Lib Kit

Illumina

• TruSeq^® Stranded Total RNA Library Prep (Human/Rat, Gold, Globin)
• Illumina^® Stranded Total RNA Prep with Ribo-Zero Plus

New England Biolabs

• NEBNext^® Ultra^TM II Directional RNA Library Prep Kit for Illumina

Roche Sequencing solutions

• KAPA^® RNA HyperPrep Kit

Takara Bio

• SMARTer^® Stranded Total RNA Sample Prep Kit - HI Mammalian
• SMARTer^® Stranded Total RNA Sample Prep Kit - Low Input Mammalian

Thermo Fisher Scientific

• Collibri^TM Stranded RNA Library Prep Kit for Illumina Systems

RNA-seq Analysis Portal supports analysis of FASTQ and BAM data generated on Thermo Fisher^® Ion Torrent^® instruments using the following kit:

QIAGEN

• QIAseq^® miRNA Library Kit

Data is analyzed using dedicated analysis workflows. Details specific to a given analysis workflow are provided in later sections. The main steps in an expression analysis are:

• Reads are aligned and counted to produce expression values for the individual samples (Align and count).
• Expression levels between groups of samples are compared in an experiment, producing one or more differential expression outputs (Create experiment).

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