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Foundry Tutorial Pipeline Specification

Pipeline Details

  • Name: Foundry Tutorial Pipeline
  • Pipeline UUID: f931qnj8l8qaosa4zywtu9hzodsp40
  • Version: 2.0.2
  • View Pipeline:

Overview

Foundry Tutorial Pipeline is designed for demonstrating how to run a comprehensive RNA-sequencing analysis pipeline in Foundry. This pipeline automates the complete workflow from raw sequencing data preprocessing through differential expression analysis, ensuring reliable and reproducible results for educational and research purposes.

Key Use cases:

  • Educational Training: Demonstrating complete RNA-seq analysis workflow for new users learning bioinformatics pipelines.
  • Differential Gene Expression Analysis: Performing comprehensive DE analysis using both DESeq2 and Limma Voom methodologies.
  • Quality Control and Preprocessing: Implementing standard QC procedures including adapter removal, quality assessment, and read alignment.

Features

  • Multiple Differential Expression Methods: Supports both DESeq2 and Limma Voom for comprehensive statistical analysis.
  • Comprehensive Quality Control: Implements FastQC for quality assessment, adapter removal using Trimmomatic, and MultiQC-style reporting.
  • STAR Alignment Integration: High-performance spliced alignment using STAR aligner with automatic index building.
  • Gene Set Enrichment Analysis: Includes GSEA module for pathway analysis and functional interpretation.
  • Flexible Read Quantification: Uses featureCounts for both gene-level and transcript-level quantification.
  • Batch Effect Handling: Built-in batch correction capabilities for PCA plots and statistical modeling.
  • Modular Design: Supports customization with conditional execution of different analysis modules.
  • Comprehensive Reporting: Generates detailed summary reports, visualizations, and QC metrics.

Input/Output Specification

Inputs

Required

Raw Sequencing Reads

  • Description: FASTQ files containing raw RNA-sequencing reads, supporting both single-end and paired-end data.
  • Format: .fastq.gz
  • Example File Path: /path/to/input/sample_R1.fastq.gz

Reference Genome Files

  • Description: Genome FASTA file and GTF annotation file for alignment and quantification.
  • Format: .fasta, .gtf
  • Example File Path: /path/to/reference/genome.fasta

Optional Inputs

Groups File

  • Description: Tab-separated metadata file containing sample information for differential expression analysis.
  • Required Columns: sample_name, group
  • Format: Tab-separated values (.tsv)
  • Example:

Sample_name group sample1 control sample2 treatment

Comparison File

  • Description: Specifies which groups to compare in differential expression analysis.
  • Required Columns: controls, treats, names
  • Format: Tab-separated values (.tsv)
  • Example:

controls treats names control treatment treatment_vs_control

Outputs

Reported Outputs

  • Differential Expression Results:
  • Description: Statistical results from DESeq2 and/or Limma Voom analysis including fold changes, p-values, and adjusted p-values
  • Format: .tsv, .html
  • Example File Path: /output/DE_analysis/treatment_vs_control_DESeq2.tsv
  • Visualization App: DE Browser

  • Location: DE_reports folder

  • Gene Count Matrix:

  • Description: Normalized and raw count matrices from featureCounts quantification
  • Format: .tsv
  • Example File Path: /output/counts/gene_id_featureCounts.tsv
  • Visualization App: DE Browser, IGV

  • Location: Count_files folder

  • GSEA Results:

  • Description: Gene set enrichment analysis results with pathway enrichment scores
  • Format: .html, .tsv
  • Example File Path: /output/GSEA/hallmark_pathways.html
  • Visualization App: GSEA Browser
  • Location: GSEA_reports folder

Supporting Outputs

  • Aligned BAM Files:
  • Description: STAR-aligned reads in BAM format with corresponding index files
  • Format: .bam, .bai

  • Example File Path: /intermediate/alignments/sample1_sorted.bam

  • Quality Control Reports:

  • Description: FastQC reports and alignment statistics from STAR
  • Format: .html, .txt

  • Example File Path: /intermediate/QC/sample1_fastqc.html

  • STAR Alignment Logs:

  • Description: Detailed alignment statistics and logs from STAR aligner
  • Format: .out, .tab, .txt
  • Example File Path: /intermediate/STAR_logs/sample1Log.final.out

Associated Processes

References & Additional Documentation