STAR NGS Pipeline

This repository contains a shell script for running a complete NGS data analysis pipeline using several bioinformatics tools, including SRA Toolkit, Trimmomatic, FastQC, STAR, and featureCounts. The pipeline performs the following steps:

1. Data Download: Downloads NGS data from SRA.
2. Quality Control: Performs quality control on raw FASTQ files using FastQC.
3. Trimming: Trims adapters and low-quality bases from the reads using Trimmomatic.
4. Mapping: Maps the trimmed reads to a reference genome using STAR.
5. Feature Counting: Counts the features using featureCounts.

Prerequisites

Before running the script, ensure that the following tools are installed on your system:

• SRA Toolkit
• Trimmomatic
• FastQC
• STAR
• Miniconda

Output

The script generates several output files, including:

FASTQ files (SRR8986990_1.fastq, SRR8986990_2.fastq)

FastQC reports (SRR8986990_1_fastqc.html, SRR8986990_2_fastqc.html)

Trimmed FASTQ files (SRR8986990_1_trimmed_paired.fastq, SRR8986990_2_trimmed_paired.fastq)

BAM file (mappingAligned.sortedByCoord.out.bam)

Feature counts file (counts_file.txt)

Notes

Ensure that the paths to the reference genome and GTF files are correct.

Modify the script as necessary to fit your specific data and analysis needs.