**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.

.. code-block:: RST

  results/
  ├── bowtie_index/
  ├── fastp/
  ├── fastqc/
  ├── mirna_quant/
  ├── mirtrace/
  ├── multiqc/
  └── pipeline_info/


The table below describes the contents of each folder -

.. list-table:: Folder with outputs
   :widths: 20 20 60
   :header-rows: 1

   * - 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**

.. list-table:: Checklist
   :widths: 30 30
   :header-rows: 1

   * - 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 <https://www.youtube.com/watch?v=qPbIlO_KWN0&ab_channel=PhilEwels>`_ for multiQC and `this <https://mugenomicscore.missouri.edu/PDF/FastQC_Manual.pdf>`_ manual for FASTQC.