FAQs

• Does this pipeline support ORA compressed FASTQs?

  • Yes, all iterations of the pipeline support analysis from .fastq.ora files.

• Can I load more than one sample at a time?

  • Yes. When selecting biosamples, multiple can be selected as long as sex is set to auto-detect.

• How long does analysis take?

  • Using DRAGEN locally, a run generally will take

    • <1hr for Germline at ~35x coverage

    • ~3 hours for Somatic WGS tumor-only at 100x coverage

    • ~4 hours for Somatic WGS tumor-normal at 100x/50x T/N coverage

• Is there demo data available?

  • Yes, there is demo data in BaseSpace, ICA, and ICM.

  • To access the demo data on BaseSpace, go to the demo data tab and search for "5-Base".

    
  • On ICA, the demo data is included in the DRAGEN 4.4 bundle. After adding the DRAGEN 4.4 bundle to a project, navigate to the data tab, and find the "Illumina DRAGEN 5-Base Methylation Germline Demo Data" folder.

  • On ICM, create a study, and click "+ Add Data" and "Select from ICA project". Select "Bulk", "Methylation", and then "Illumina 5-Base Solution" as the format. Click "+ Add Demo Data", and navigate to the "Multiomics-Demo-Data" folder. Click into "Methylation", then "Illumina-5-base-solution", and import all samples in that folder.

  

  

  
• How does DRAGEN tell when a site is a genetic variant, or a methylated site?

  • A genetic variant impacts two strands of the DNA; a methylated site impacts only one.

    
• What DRAGEN features are 5-base aware?

  • Only the features and options specified in this documentation are formally supported. All other features should be considered experimental and used at risk.

  • For additional information, review the DRAGEN documentation: https://help.connected.illumina.com/dragen/product-guide/dragen-v4.4/dragen-methylation-pipeline/dragen-5base-pipeline#summary

• How does DRAGEN 5-Base in Germline, Somatic, and Enrichment differ from DRAGEN Methylation?

  • In general, it's not recommended to use DRAGEN Methylation for 5-Base is because DRAGEN Methylation is meant for bisulfite data (unmethylated C -> T), and not our 5-Base solution (where you convert methylated C -> T). DRAGEN Methylation doesn't allow for variant calling with the 5-Base library. Additionally, the alignment isn’t 5-Base aware, and thus will be worse than when running DRAGEN Germline, Somatic, or Enrichment. However, there is a need to do a direct comparison between bisulfite data and 5-base, it is possible to run 5-Base libraries on DRAGEN Methylation.

• Should DRAGEN Germline, Somatic, and Enrichment be used for non-human samples?

  • Methylation calling for non-human samples is supported within DRAGEN Germline, Somatic, and Enrichment. Variant calling for non-human samples is not formally validated in these apps, but can be done experimentally. Some non-mammalian species have high CpH methylation; to support these samples, it's recommended to run --enable-cpg-methylated-mapping=false in the "Additional Arguments" section of the App. This setting is not recommended for analysis of samples where the majority of methylation occurs in a CpG context.