star-alignment

Align RNA-seq reads with STAR for novel junction discovery.

6|2|Updated Jun 11, 2026

Search Tags:#alignment #RNA-seq #STAR #novel junction #2-pass mapping

Ready to run

npx skills add https://github.com/pradyumnasagar/open-research-skills --skill star-alignment

💬 Prompt for ChatGPT / Claude Chat▼

Please help me install this Agent Skill.
Skill: star-alignment
Source: https://github.com/pradyumnasagar/open-research-skills/tree/main/skills/bioinformatics-sequence/star-alignment
Command: npx skills add https://github.com/pradyumnasagar/open-research-skills --skill star-alignment

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill requires STAR, samtools, and includes scripts (resource) and references (resource) components.

What problem does it solve?

This Skill aligns RNA-seq reads with STAR, a powerful aligner for novel junction discovery, providing 2-pass mapping and genome-generation strategies.

Core Features & Use Cases

Splice-aware Alignment: Aligns RNA-seq reads with high sensitivity to novel junctions.
2-pass Mapping: Offers 2-pass mapping for sensitive novel junction discovery.
Genome Generation: Generates genome index for alignment.
Use Case: Ideal for bulk RNA-seq with novel junction discovery, single-cell RNA-seq, chimeric/fusion detection, and long-read cDNA/ONT direct RNA.

Quick Start

Generate the genome index with 'STAR --runMode genomeGenerate' and align reads with 'STAR --runMode alignReads'.

Frequently Asked Questions about star-alignment

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

FAQPage Schema

How does 2-pass mapping improve RNA-seq alignment for novel junction discovery?▼

STAR aligner supports bulk RNA-seq, single-cell RNA-seq, chimeric transcript and fusion detection, and long-read cDNA or ONT direct RNA sequencing, applying splice-aware alignment to discover novel junctions across these varied sequencing modalities.

How do I generate a genome index and align RNA-seq reads with STAR?▼

STAR alignment requires the STAR aligner, samtools, and appropriate reference genome annotations. You must have these dependencies installed and have your reference genome files prepared before generating the genome index and aligning RNA-seq reads.

What is the best way to detect chimeric transcripts and fusion genes from RNA-seq data?▼

The best way to detect chimeric transcripts and fusion genes is using splice-aware RNA-seq alignment with STAR. It provides high sensitivity for novel junction discovery and explicitly supports chimeric and fusion detection across bulk and long-read RNA-seq datasets.

Can I use STAR for long-read cDNA and ONT direct RNA alignment?▼

Yes, STAR is applicable for long-read cDNA and ONT direct RNA alignment. It performs splice-aware alignment on these long-read formats, supporting novel junction discovery and chimeric transcript detection alongside standard bulk RNA-seq workflows.