Results from smRNA-seq
After running the small RNA-seq workflow using Nextflow, the following output folders are generated. These include quality control reports, trimmed reads, small RNA quantification results, and summary statistics for traceability and reproducibility.
results/
├── bowtie_index/
├── fastp/
├── fastqc/
├── mirna_quant/
├── mirtrace/
├── multiqc/
└── pipeline_info/
The table below describes the contents of each folder -
Folder |
Contents |
Description |
|---|---|---|
bowtie_index/ |
Bowtie index files (.ebwt) |
Pre-built or generated Bowtie index files used for aligning small RNAs to reference genome or miRBase sequences. |
fastp/ |
Trimmed FASTQ files, .html, .json |
Quality-filtered and adapter-trimmed reads processed by fastp, along with HTML and JSON reports for per-sample quality metrics. |
fastqc/ |
.html, .zip |
Quality control reports from FastQC on raw (pre-trimmed) reads. |
mirna_quant/ |
.tsv, .txt, .csv |
miRNA quantification tables (read counts, TPM/CPM) generated by tools like miRDeep2, sRNAbench, or custom scripts. May include read mapping summaries and annotations. |
mirtrace/ |
.html, .csv, .txt |
Quality control and contamination assessment from miRTrace, identifying species-of-origin, RNA class contamination (tRNA, rRNA, etc.), and length distributions. |
multiqc/ |
multiqc_report.html |
Aggregated QC summary from FastQC, fastp, and miRTrace, all in one report. |
pipeline_info/ |
.log, .yaml, .txt |
Workflow execution metadata, including software versions, run parameters, and Nextflow logs. Useful for reproducibility. |
Exploring the Outputs
Open HTML reports (fastqc/.html, fastp/.html, mirtrace/*.html, multiqc/multiqc_report.html) in your browser for visual inspection.
Examine read counts in mirna_quant/ to check for the most abundant miRNAs or total read distribution.
Use grep, cut, or pandas to parse quantification files and generate plots.
Output Validation Checklist
Checkpoint |
Expected outcome |
|---|---|
FastQC quality scores |
> Q30 in most regions |
Fastp adapter removal |
Adapter content largely eliminated |
miRTrace contamination |
High percentage of reads mapping to expected organism; minimal tRNA/rRNA contamination |
miRNA quantification |
Consistent expression of known abundant miRNAs |
MultiQC report |
No critical QC failures; helpful visual summary |
To explore more in-depth explanations for interpreting your FASTQC and multiQC reports, you can use this video link for multiQC and this manual for FASTQC.