> For the complete documentation index, see [llms.txt](https://knowledge.illumina.com/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://knowledge.illumina.com/software/dragen/software-dragen-faq-list/000010217.md).

# 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](https://www.illumina.com/products/by-type/informatics-products/dragen-secondary-analysis.html)
* [DRAGEN RNA Product page](https://www.illumina.com/products/by-type/informatics-products/basespace-sequence-hub/apps/dragen-rna.html)
* [DRAGEN Differential Expression Product Page](https://www.illumina.com/products/by-type/informatics-products/basespace-sequence-hub/apps/dragen-differential-expression.html)
* DRAGEN RNA support documentation:
  * [Software downloads](https://support.illumina.com/sequencing/sequencing_software/dragen-bio-it-platform/downloads.html)
  * [DRAGEN applications](https://help.dragen.illumina.com/overview/key-applications)
  * [DRAGEN RNA pipeline](https://help.dragen.illumina.com/dragen-v4.5/product-guides/dragen-v4.5/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](https://www.illumina.com/products/by-type/informatics-products/connected-multiomics/order.html).

**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](https://www.illumina.com/content/dam/illumina/gcs/assembled-assets/marketing-literature/novaseq-x-software-ecosystem-tech-note-m-gl-01587/novaseq-x-software-ecosystem-tech-note-m-gl-01587.pdf), and the DRAGEN Bio-IT Platform onboard the NextSeq 1000 and NextSeq 2000 systems data sheet, [here](https://www.illumina.com/content/dam/illumina/gcs/assembled-assets/marketing-literature/dragen-onboard-nextseq-data-sheet-m-gl-00729/dragen-onboard-nextseq-data-sheet-m-gl-00729.pdf).

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| *For any feedback or questions regarding this article (Illumina Knowledge Article #10217), contact Illumina Technical Support* [*techsupport@illumina.com*](mailto:techsupport@illumina.com?subject=Question%2FFeedback%20Regarding%20Illumina%20Knowledge%20Article%20#000010217%20-%20Software%20\&body=Dear%20Illumina%20Technical%20Support,%0D%0A%0D%0A)*.* |


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