Bulk RNA-seq Analysis

This repository contains quality control reports, count matrices, scripts, and visualizations from bulk RNA-seq analysis. It provides a reproducible workflow for RNA-seq data processing and visualization.

This study focuses on comparing gene expression patterns between Black Rice (Oryza sativa indica) and White Rice (Oryza sativa japonica). The datasets include transcript and gene counts for both rice types, along with quality control metrics and visualizations.

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Repository Structure

RNAseq_Analysis/
│
├── 01_QC_Reports/ # FastQC HTML reports for sequencing reads
├── 02_QC_Plots/ # PNG visualizations for quality metrics
├── 03_Count_Matrices/ # Transcript/gene count matrices & scripts
│ ├── transcript_count_matrix.csv
│ ├── nuclear_gene_count_matrix.csv
│ ├── Organelle_gene_count_matrix.xlsx
│ ├── prepDE.py
│ └── Bulk_RNA_seq.sh
├── 04_Heatmaps/ # Heatmaps of gene expression patterns
│ ├── Transcript_Heatmap.png
│ ├── Nuclear_Gene_Heatmap.png
│ └── Organelle_Heatmap.png
└── README.md

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Tools Used

• FastQC: Quality control for raw sequencing reads
• Python (prepDE.py): Extract transcript/gene count matrices
• Bash (Bulk_RNA_seq.sh): Automates RNA-seq workflow
• Visualization Tools: Heatmaps and QC plots, performed in IDEp and Python

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Study Overview

• Species:

  • Black Rice: Oryza sativa indica
  • White Rice: Oryza sativa japonica

• Objective: Identify differential gene expression patterns between Black Rice and White Rice.

• Data: Raw RNA-seq reads, QC metrics, transcript and gene count matrices, and heatmaps.

• Methodology:

  • Performed bulk RNA-seq of Oryza sativa (pigmented vs. non-pigmented)
  • Processed ∼17 million paired-end reads via Linux pipelines
  • Analyzed large-scale sequencing data for quality and expression patterns

• Analysis Steps:

  1. Assess sequencing quality (FastQC reports & QC plots)
  2. Generate transcript/gene count matrices using prepDE.py
  3. Visualize expression patterns via heatmaps

Transcript	Nuclear	Organelle

4. Compare gene expression between the two rice types