# 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.                                                                       |