skills.rest
Starlitnightly
StarlitnightlyCOMMUNITY
Explore all skills by this author →
GitHub

fastq-analysis-pipeline

Orchestrate RNA-seq analysis from FASTQ files to gene count matrices.

32|5|Updated Mar 12, 2026
Search Tags:#bioinformatics#alignment#rna-seq#quantification#star#fastq#kallisto
One-click install
npx skills add https://github.com/Starlitnightly/omicclaw --skill fastq-analysis-pipeline
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: fastq-analysis-pipeline
Source: https://github.com/Starlitnightly/omicclaw/tree/main/src/omicverse_skills/skills/fastq-analysis
Command: npx skills add https://github.com/Starlitnightly/omicclaw --skill fastq-analysis-pipeline

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill includes scripts (resource) and references (resource) components.

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'.

Frequently Asked Questions about fastq-analysis-pipeline

High-intent search queries and answers about installing and using this skill.

FAQPage Schema
How do I process raw FASTQ files for RNA-seq alignment and quantification?▼

RNA-seq FASTQ processing involves quality control, genome alignment, and quantification. This pipeline orchestrates the complete workflow using fastp, STAR, and featureCounts to generate gene count matrices from raw sequencing files.

Can I download SRA data and run it through a bulk RNA-seq pipeline automatically?▼

Yes, SRA data acquisition is built into the RNA-seq pipeline. You can input SRA IDs directly, and the pipeline will download the raw FASTQ files, perform QC, and align reads to a reference genome automatically.

Does this RNA-seq quantification workflow support single-cell data?▼

Yes, the RNA-seq quantification workflow supports single-cell RNA sequencing. It utilizes kallisto and bustools to process single-cell FASTQ files and generate gene count matrices for downstream analysis.

What is the best way to align RNA-seq reads to a reference genome?▼

Aligning RNA-seq reads to a reference genome is best handled by the STAR aligner. The pipeline coordinates STAR alignment using reference genome FASTA and GTF files to accurately map sequencing reads.

Do I need local FASTQ files to start the RNA-seq alignment pipeline?▼

No, local FASTQ files are not strictly required to start the RNA-seq alignment pipeline. The pipeline supports flexible input, allowing you to start directly from SRA IDs or use local FASTQ files if available.

Why use kallisto and bustools for RNA-seq quantification instead of featureCounts?▼

Kallisto and bustools are used for single-cell RNA-seq quantification, while featureCounts handles bulk RNA-seq. The pipeline selects the appropriate quantification method based on your specific sequencing data type.

Related Skills

Explore More Data & Analytics Skills→
sun2443sun2443

nextflow-development

Run nf-core bioinformatics pipelines on sequencing data with environment validation and output verification.

Community
Advanced
omicverseomicverse
32

bulk-rna-seq-differential-expression-with-omicverse

Analyze bulk RNA-seq count matrices for differential expression and pathway enrichment.

Official
Advanced
Revelo-RNASeqRevelo-RNASeq

bio-workflows-rnaseq-to-de

Automates RNA-seq pipeline from FASTQ files to differential expression with DESeq2 and Salmon or STAR+featureCounts.

Official
Advanced
omicverseomicverse
32

fastq-analysis-pipeline

Produce aligned BAM files and gene count matrices from SRA or FASTQ inputs.

Official
Advanced