Analysis options FAQ for Illumina Rapid RNA Kits

What are options for secondary and tertiary analysis of Rapid RNA Prep data?

Secondary Analysis

The DRAGEN RNA App is available in Illumina cloud computing environments, such as BaseSpace Sequence Hub (BSSH). It is available for DRAGEN onboard on the NovaSeq X Series and NextSeq 1000/2000 instruments currently.

For additional information, see:

• Learn more about DRAGEN secondary analysis

• DRAGEN RNA Product page

• DRAGEN Differential Expression Product Page

• DRAGEN RNA support documentation:

  • Software downloads

  • DRAGEN applications

  • DRAGEN RNA pipeline

Tertiary Analysis

For the tertiary analysis of Illumina Rapid RNA Prep data, Illumina recommends Illumina Connected Multiomics. Illumina Connected Multiomics is a powerful and intuitive cloud-based solution that enables multiomic data analysis and visualization at scale. Learn more about Illumina Connected Multiomics software, here.

What are the newest features of DRAGEN RNA?

RNA Gene Fusion

v4.4.4 introduced a new model for splice variant calling and made significant improvements in Gene Fusion calling. v4.4.6 further adds minor improvements, including improvements for RNA amplicon panels.

• Splice variant calling

• Fix for splice variant not called on NSD1 gene

• Add NPM1 to repeat-intervals BED file for fusion

• RNA amplicon and WTS updated to use same parameters

• Fix for splice variant fusions not found in fusion_candidates.final

• Gene Fusion

• Add NoAssembly for readthrough fusions

• Improve checks for existence of enriched gene/region input files

• Add FUSION_SEQ, FUSION_SEQ_LEN, FUSION_LEEWAY to VCF output

• Quantification

• Add RNA quantification metrics to metrics.json output, so that quant.metrics.csv values are propagated over

Bulk RNA v4.5

• Partial Tandem Duplications (PTD)/nternal Tandem Duplications (ITD) detection in the Bulk RNA fusion caller — Beta

• The gene fusion caller now supports detection of Partial Tandem Duplications (PTD) and Internal Tandem Duplications (ITD), intragenic self-fusions relevant to oncology applications.

• Specify genes for PTD/ITD detection: --rna-gf-ptd-genes="KMT2A FGFR1" (default: empty; standard intragenic events filtered) Validated for KMT2A PTD detection. Tagged as Beta.

• DRAGEN Universal Annotation Parser (DUAP)

• DRAGEN now includes a universal annotation parser compatible with all major annotation sources: GENCODE, Ensembl, RefSeq, and custom annotations.

• Supports both GTF and GFF3 formats. Selective analysis using a BED file (eg, for panel workflows).

• Provides flexibility in defining which features are included in the analysis, with advanced filtering by transcript and intron length.

• Reduces annotation preprocessing requirements and simplifies custom reference workflows for RNA analysis.

Where is there more information about DRAGEN Onboard analysis for the NovaSeq X Series and NextSeq 1000/2000?

See the The NovaSeq X Series software ecosystem technical note, here, and the DRAGEN Bio-IT Platform onboard the NextSeq 1000 and NextSeq 2000 systems data sheet, here.

For any feedback or questions regarding this article (Illumina Knowledge Article #10217), contact Illumina Technical Support [e-mail].