fastq-analysis-pipeline

What problem does it solve?

This Skill streamlines the complex process of analyzing raw FASTQ sequencing data, from initial quality control and alignment to gene quantification for both bulk and single-cell RNA sequencing experiments.

Core Features & Use Cases

• End-to-End Pipeline: Manages SRA downloading, quality control (fastp), alignment (STAR), and quantification (featureCounts or kallisto/bustools).
• Flexible Input: Works with SRA IDs or local FASTQ files.
• Use Case: Analyze raw RNA-seq data from public SRA archives, perform quality checks, align reads to a reference genome, and generate gene count matrices for downstream differential expression analysis.

Quick Start

Run the complete bulk RNA-seq pipeline starting from SRA IDs 'SRR1234567' and 'SRR1234568', aligning to the genome specified by 'reference/genome.fa' and 'reference/genes.gtf'.