# 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.

<figure><img src="/files/65mK0sCJvwbfld8yzSNF" alt=""><figcaption></figcaption></figure>

* How long does DRAGEN analysis take?

  | DRAGEN Germline   | 1 sample                      | 35x      | Germline, 5-base methylation calling, SNV, CNV, SV | \~1h    |
  | ----------------- | ----------------------------- | -------- | -------------------------------------------------- | ------- |
  | DRAGEN Somatic    | 1 sample (tumor-only)         | 100x     | Somatic, 5-base methylation calling, SNV           | \~3h15m |
  | DRAGEN Somatic    | 2 samples (tumor-normal pair) | 100x/50x | Somatic, 5-base methylation calling, SNV           | \~4h45m |
  | DRAGEN Somatic    | 2 samples (tumor-normal pair) | 100x/50x | Somatic, 5-base methylation calling, CNV, SV       | \~5h    |
  | DRAGEN Somatic    | 2 samples (tumor-normal pair) | 100x/50x | Somatic, 5-base methylation calling, SNV, CNV, SV  | \~6h30m |
  | DRAGEN Enrichment | 1 sample                      | 2500x    | Somatic UMI Liquid, SNV                            | \~30m   |
* 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".<br>

    <figure><img src="/files/XrS2KTwFWwMfuOoZxTGt" alt=""><figcaption></figcaption></figure>
  * 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.

  <br>

  <figure><img src="/files/TD7Abtok9a1SmkgV2eod" alt=""><figcaption></figcaption></figure>

  <figure><img src="/files/nJwCbdeP3Su8vBnNcOXm" alt=""><figcaption></figcaption></figure>

  <figure><img src="/files/C6pvHJjkhRcU6Oqvkb5O" alt=""><figcaption></figcaption></figure>
* 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.<br>

    <figure><img src="/files/aghXT3lQEFVYl2sFvAV3" alt=""><figcaption></figcaption></figure>
* 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.


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