Align and count - Demultiplexed RNA sample kits
This Align and count analysis workflow is used for the remaining sample kits. These do not leverage unique molecular indexes. Sample data must be demultiplexed prior to being uploaded to RNA-seq Analysis Portal.
Sample kits
- QIAseq Stranded mRNA Select/Stranded Total RNA Lib Kit (QIAGEN)
- QIAseq FastSelect RNA Lib Kit (QIAGEN)
- QIAseq UPX 3' Transcriptome Kit (with already-demultiplexed input data selected)
- QIAseq UPXome RNA Lib Kit (with already-demultiplexed input data selected)
- TruSeq Stranded Total RNA Library Prep (Human/Rat, Gold, Globin)(Illumina)
- Illumina Stranded Total RNA Prep with Ribo-Zero Plus (Illumina)
- NEBNext UltraTM II Directional RNA Library Prep Kit for Illumina (New England Biolabs)
- KAPA RNA HyperPrep Kit (Roche Sequencing solutions)
- SMARTer Stranded Total RNA Sample Prep Kit - HI Mammalian/Low Input Mammalian (Takara Bio)
- Collibri Stranded RNA Library Prep Kit for Illumina Systems (Thermo Fisher Scientific)
The analysis workflow includes the steps below. Parameters for the individual sample kits are listed in Appendix C.
- Trim Reads. Low quality and ambiguous nucleotides and adapter sequences are removed.
- RNA-Seq Analysis. Reads are mapped to transcripts, and expression values for each gene are obtained by summing the transcript counts belonging to the gene.
The tools are described in more detail in the QIAGEN CLC Genomics Workbench manual:
- https://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/2103/index.php?manual=Trim_Reads.html
- https://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/2103/index.php?manual=RNA_Seq_Analysis.html