Bulk RNA-seq Analysis

This repository contains scripts and data for bulk RNA-seq analysis. The primary script included is used to run FastQC, a quality control tool for high throughput sequence data.

FastQC Analysis

FastQC is a popular tool for assessing the quality of sequencing data. It provides a simple way to perform quality control checks on raw sequence data coming from high throughput sequencing pipelines.

Script: run_fastqc.sh

The run_fastqc.sh script automates the process of running FastQC on a set of FASTQ files. It processes multiple files and generates quality control reports for each one.

Usage

1. Directory Structure:

   • Place your FASTQ files in a directory. In this example, they are located in /home/tigs/Downloads/venki/Bulk_rna_seq/data.

2. Script Location:

   • The script should be placed in an accessible location. You can modify the paths within the script as needed.

3. Running the Script:

   • Ensure the script is executable by running:

     chmod +x run_fastqc.sh

   • Execute the script:

     ./run_fastqc.sh

Script Details

#!/bin/bash

# Directory containing the FASTQ files
INPUT_DIR="path to directory"

# Output directory for FastQC results
OUTPUT_DIR="path to directory"

# Create output directory if it doesn't exist
mkdir -p "$OUTPUT_DIR"

# List of file prefixes to process
FILES=("SRR5223500_1" "SRR5223500_2" "SRR5223505_1" "SRR5223505_2" "SRR5223522_1" "SRR5223522_2")

# Loop through each file prefix and run FastQC
for file in "${FILES[@]}"; do
    echo "Processing ${file}.fastq"
    fastqc -o "$OUTPUT_DIR" "$INPUT_DIR/${file}.fastq"
done

echo "FastQC analysis complete."

This repository contains scripts and data for bulk RNA-seq analysis. The primary scripts included are used to run fastp and FastQC, tools for quality control and preprocessing of high throughput sequence data.

fastp Analysis

This repository includes scripts and data for bulk RNA-seq analysis, with a focus on using fastp for quality control and preprocessing of high throughput sequencing data.

fastp Overview

fastp is a tool designed for fast all-in-one preprocessing for FastQ files. It provides extensive statistics and generates visualizations to help researchers quickly evaluate the quality of their sequencing data.

Script: run_fastp.sh

The run_fastp.sh script automates the process of running fastp on a set of paired-end FASTQ files.

Usage

1. Directory Structure:

   • Place your paired-end FASTQ files in a directory. For example, /home/tigs/Downloads/venki/Bulk_rna_seq/data.

2. Running the Script:

   • Ensure the script is executable:

     chmod +x run_fastp.sh

   • Execute the script:

     ./run_fastp.sh

Script Details

#!/bin/bash

# Directory containing the paired-end FASTQ files
INPUT_DIR="path to directory"

# Output directory for fastp results
OUTPUT_DIR="path to directory"

# Create output directory if it doesn't exist
mkdir -p "$OUTPUT_DIR"

# List of file prefixes to process
FILES=("SRR5223500" "SRR5223505" "SRR5223522")

# Loop through each file prefix and run fastp
for file in "${FILES[@]}"; do
    echo "Processing ${file}_1.fastq and ${file}_2.fastq"
    fastp -i "$INPUT_DIR/${file}_1.fastq" -I "$INPUT_DIR/${file}_2.fastq" \
          -o "$OUTPUT_DIR/${file}_1_clean.fastq" -O "$OUTPUT_DIR/${file}_2_clean.fastq" \
          -h "$OUTPUT_DIR/${file}_fastp.html" -j "$OUTPUT_DIR/${file}_fastp.json"
done

echo "fastp analysis complete."