Appendix C - Analysis workflow versions, species support and parameters

This appendix provides information on analysis workflow and sample comparability, gives an overview of analysis workflow versions and species support, and lists secondary analysis workflow parameters for the individual sample kits and analyses.


About analysis workflow versions and sample comparability

To ensure comparability of samples within a project, the analysis workflow version for a specific sample kit-reference combination is restricted to a single version. As an example, if QIAseq Stranded mRNA Select/Total RNA Lib Kit, Homo sapiens (GRCh38.103) samples were included in Project A in RNA-seq Analysis Portal 1.0, Project A will be locked to the analysis workflow version of RNA-seq Analysis Portal 1.0, i.e. v1.0. Consequently, QIAseq Stranded mRNA Select/Total RNA Lib Kit, Homo sapiens (GRCh38.103) samples added to this project at a later point in time will be processed with analysis workflow 1.0 regardless the version of RNA-seq Analysis Portal.

If you create a new project in the Align and count dialog, samples will be processed with the most recent analysis workflow version.

To have samples processed with an older analysis workflow version, e.g. to ensure that they can be included in experiments with older samples, in the Align and count dialog select an existing project with samples processed with the desired analysis workflow version.

The version of the analysis workflow with which samples were processed can be found from the Experiment summary tab of the Sample and Quality control, as well as from the Samples page.


Analysis workflow versions in RNA-seq Analysis Portal

Table 2 provides an overview of the most recent sample kit analysis workflow versions in each version of RNA-seq Analysis Portal.


Table 2: Overview of most recent sample kit analysis workflow versions in each version of RNA-seq Analysis Portal.
RNA-seq Analysis Portal version 1.0 1.1 2.0 2.5 3.0 3.0.1 4.0
QIAseq miRNA Library Kit v1.0 v1.0 v1.1 v1.2 v1.2 v1.2 v1.2
QIAseq UPX 3' Transcriptome Kit v1.0 v1.0 v1.1 v1.2 v1.2 v1.2 v1.2
QIAseq UPXome RNA Lib Kit       v1.0 v1.0    
QIAseq UPXome RNA Lib Kit (N6-T RT + ODT-T RT primers)           v1.0 v1.0
QIAseq UPXome RNA Lib Kit (ODT-T RT primer)           v1.0 v1.0
QIAseq UPXome RNA Lib Kit (N6-T RT primer)           v1.0 v1.0
QIAseq FastSelect RNA Lib Kit (N6-T RT + ODT-T RT primers)             v1.0
QIAseq FastSelect RNA Lib Kit (ODT-T RT primers)             v1.0
QIAseq FastSelect RNA Lib Kit (N6-T RT)             v1.0
QIAseq Stranded mRNA Select/Stranded Total RNA Lib Kit v1.0 v1.1 v1.2 v1.2 v1.2 v1.2 v1.2
TruSeq Stranded Total RNA Library Prep   v1.0 v1.1 v1.1 v1.1 v1.1 v1.1
Illumina Stranded Total RNA Prep   v1.0 v1.1 v1.1 v1.1 v1.1 v1.1
NEBNext Ultra II Directional RNA Library Prep Kit   v1.0 v1.1 v1.1 v1.1 v1.1 v1.1
KAPA RNA HyperPrep Kit   v1.0 v1.1 v1.1 v1.1 v1.1 v1.1
SMARTer Stranded Total RNA Sample Prep Kit   v1.0 v1.1 v1.1 v1.1 v1.1 v1.1
Collibri Stranded RNA Library Prep Kit   v1.0 v1.1 v1.1 v1.1 v1.1 v1.1



Sample kit analysis workflows and species support

Species support depends on the sample kit analysis workflow. Table 3 gives an overview of species support for the two categories of analysis workflows, miRNA and RNA:

Biological insights support. Table 3 also indicates whether biological insights are supported. For species other than human, mouse and rat, Ingenuity Pathway Analysis (IPA) will map the gene identifiers according to HomoloGene to the corresponding human, mouse, and rat ortholog information in the QIAGEN Knowledge Base. Therefore, biological insights results will reflect content for human, mouse, and rat.


Table 3: Species support for miRNA and RNA analysis workflows.
  miRNA Biological insights for miRNA RNA Biological insights for RNA
Arabidopsis thaliana x   x  
Bos taurus x   x x
Caenorhabditis elegans x   x  
Canis lupus familiaris x   x  
Danio rerio x   x x
Drosophila melanogaster x   x x
Equus caballus x   x  
Gallus gallus x   x x
Homo sapiens x x x x
Macaca fascicularis     x  
Macaca mulatta x   x x
Mus musculus x x x x
Oncorhynchus mykiss     x  
Oryctolagus cuniculus x   x  
Rattus norvegicus x x x x
Saccharomyces cerevisiae     x  
Schizosaccharomyces pombe     x  
Sus scrofa x   x  




Subsections