# Secondary Analysis Results

### Folder structure

Outputs are split in three main folders:

* counts
* fastqc
* reports

#### File and Folder Structure (`counts/`)

The `counts/` directory contains the following subfolders and files:

| `annotation_logs/`                          | Annotation log files                                                                                                                                                                                                                                                                                                                                                            |
| ------------------------------------------- | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
| `mapping_logs/`                             | Mapping log files                                                                                                                                                                                                                                                                                                                                                               |
| `<Sample_ID>/`                              | Run parameters for each sample (`<Sample_ID>`)                                                                                                                                                                                                                                                                                                                                  |
| `READs/`                                    | <p>Read count files by RNA type, e.g.:</p><ul><li><code>all\_samples.concatenated.allRNAs.READs.txt</code></li><li><code>all\_samples.miRNA.READs.txt</code></li><li><code>all\_samples.mRNA.READs.txt</code></li><li><code>all\_samples.otherRNA.READs.txt</code></li><li><code>all\_samples.piRNA.READs.txt</code></li><li><code>all\_samples.tRNA.READs.txt</code></li></ul> |
| `run_logs/`                                 | Logs from the counting step                                                                                                                                                                                                                                                                                                                                                     |
| `UMIs/`                                     | <p>UMI count files by RNA type, e.g.:</p><ul><li><code>all\_samples.concatenated.allRNAs.UMIs.txt</code></li><li><code>all\_samples.miRNA.UMIs.txt</code></li><li><code>all\_samples.mRNA.UMIs.txt</code></li><li><code>all\_samples.otherRNA.UMIs.txt</code></li><li><code>all\_samples.piRNA.UMIs.txt</code></li><li><code>all\_samples.tRNA.UMIs.txt</code></li></ul>        |
| `all_samples.notCharacterized_mappable.txt` | Metrics for uncharacterized mappable reads                                                                                                                                                                                                                                                                                                                                      |
| `all_samples.summary.txt`                   | Summary metrics for all samples (text format)                                                                                                                                                                                                                                                                                                                                   |
| `all_samples.V1.summary.xlsx`               | Summary metrics for all samples and counts files as tabs for all RNA types (Excel format)                                                                                                                                                                                                                                                                                       |
|                                             |                                                                                                                                                                                                                                                                                                                                                                                 |

The `fastqc/` directory contains subfolders and files generated by FastQC quality control analysis. Each sequencing sample has its own `<Sample_ID>`-specific outputs, including both an interactive HTML report and a tab-delimited metrics file.

| `<Sample_ID>_fastqc/`         | <p>Subfolder containing FastQC output files for a given sample.<br><strong>Example:</strong> <code>QK2\_S2\_L001\_R1\_001\_fastqc/</code></p>   |
| ----------------------------- | ----------------------------------------------------------------------------------------------------------------------------------------------- |
| `<Sample_ID>_fastqc_data.txt` | <p>Tab-delimited summary of FastQC metrics for a sample.<br><strong>Example:</strong> <code>QK2\_S2\_L001\_R1\_001\_fastqc\_data.txt</code></p> |
| `<Sample_ID>_fastqc.html`     | <p>Interactive FastQC report (HTML format) for a sample.<br><strong>Example:</strong> <code>QK2\_S2\_L001\_R1\_001\_fastqc.html</code></p>      |

The `report/` directory contains per-sample subfolders along with an aggregated HTML report generated by DRAGEN.

| `<Sample_ID>/`                               | <p>Subfolder containing DRAGEN output files for a given sample.<br><strong>Example:</strong> <code>QK2\_S2/</code>, <code>QL4\_S4/</code></p> |
| -------------------------------------------- | --------------------------------------------------------------------------------------------------------------------------------------------- |
| `<Sample_ID>/<Sample_ID>.bowtie_metrics.csv` | sample level mapping metrics                                                                                                                  |
| `<Sample_ID>/<Sample_ID>.fastqc_metrics.csv` | sample level fastq quality metrics                                                                                                            |
| `DRAGEN_Reports.html`                        | Consolidated interactive report summarizing metrics across all samples.                                                                       |


---

# Agent Instructions: Querying This Documentation

If you need additional information that is not directly available in this page, you can query the documentation dynamically by asking a question.

Perform an HTTP GET request on the current page URL with the `ask` query parameter:

```
GET https://help.connected.illumina.com/dragen-mirna/analysis-results/secondary-analysis-results.md?ask=<question>
```

The question should be specific, self-contained, and written in natural language.
The response will contain a direct answer to the question and relevant excerpts and sources from the documentation.

Use this mechanism when the answer is not explicitly present in the current page, you need clarification or additional context, or you want to retrieve related documentation sections.