Genomics Analysis Guide

Overview

Genomic data analysis is the computational backbone of modern molecular biology. From identifying disease-associated variants through Genome-Wide Association Studies (GWAS) to quantifying gene expression with RNA-seq, these workflows transform raw sequencing data into biological insights that drive discoveries in medicine, agriculture, and evolutionary biology.

This guide covers the three most common genomic analysis workflows: RNA-seq differential expression analysis, GWAS for variant-trait associations, and variant calling from whole-genome sequencing (WGS) data. Each workflow is described with tool recommendations, command-line examples, and downstream analysis steps in R and Python.

The emphasis is on reproducibility and best practices. Genomic analyses involve many sequential steps, and errors in early stages propagate through the entire pipeline. Following standardized workflows -- like those from the Broad Institute, ENCODE, and Bioconductor -- reduces the risk of methodological errors.

RNA-seq Analysis Pipeline

Workflow Overview

Raw FASTQ files
    |
    v
[Quality Control] --> FastQC, MultiQC
    |
    v
[Trimming] --> Trimmomatic, fastp
    |
    v
[Alignment] --> STAR, HISAT2
    |
    v
[Quantification] --> featureCounts, Salmon
    |
    v
[Differential Expression] --> DESeq2, edgeR
    |
    v
[Pathway Analysis] --> clusterProfiler, GSEA

Step 1: Quality Control

# Run FastQC on all FASTQ files
fastqc -t 8 -o qc_results/ raw_data/*.fastq.gz

# Aggregate QC reports
multiqc qc_results/ -o multiqc_report/

Step 2: Read Trimming

# fastp for quality trimming and adapter removal
fastp \
  --in1 sample_R1.fastq.gz \
  --in2 sample_R2.fastq.gz \
  --out1 trimmed_R1.fastq.gz \
  --out2 trimmed_R2.fastq.gz \
  --detect_adapter_for_pe \
  --thread 8 \
  --html fastp_report.html

Step 3: Alignment with STAR

# Build genome index (one time)
STAR --runMode genomeGenerate \
  --genomeDir star_index/ \
  --genomeFastaFiles genome.fa \
  --sjdbGTFfile annotations.gtf \
  --runThreadN 16

# Align reads
STAR --runMode alignReads \
  --genomeDir star_index/ \
  --readFilesIn trimmed_R1.fastq.gz trimmed_R2.fastq.gz \
  --readFilesCommand zcat \
  --outSAMtype BAM SortedByCoordinate \
  --quantMode GeneCounts \
  --outFileNamePrefix sample_ \
  --runThreadN 16