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/	Read count files by RNA type, e.g.: all_samples.concatenated.allRNAs.READs.txt all_samples.miRNA.READs.txt all_samples.mRNA.READs.txt all_samples.otherRNA.READs.txt all_samples.piRNA.READs.txt all_samples.tRNA.READs.txt
run_logs/	Logs from the counting step
UMIs/	UMI count files by RNA type, e.g.: all_samples.concatenated.allRNAs.UMIs.txt all_samples.miRNA.UMIs.txt all_samples.mRNA.UMIs.txt all_samples.otherRNA.UMIs.txt all_samples.piRNA.UMIs.txt all_samples.tRNA.UMIs.txt
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/	Subfolder containing FastQC output files for a given sample. Example: QK2_S2_L001_R1_001_fastqc/
<Sample_ID>_fastqc_data.txt	Tab-delimited summary of FastQC metrics for a sample. Example: QK2_S2_L001_R1_001_fastqc_data.txt
<Sample_ID>_fastqc.html	Interactive FastQC report (HTML format) for a sample. Example: QK2_S2_L001_R1_001_fastqc.html

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

<Sample_ID>/	Subfolder containing DRAGEN output files for a given sample. Example: QK2_S2/, QL4_S4/
<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.