---
name: star-rnaseq-aligner-21fac3e4cc9c
description: STAR alignment skill for splice-aware RNA-seq read mapping with comprehensive QC metrics
allowed-tools:
  - Read
  - Write
  - Glob
  - Grep
  - Edit
  - WebFetch
  - WebSearch
  - Bash
metadata:
  version: "1.0"
  category: bioinformatics
  tags:
    - transcriptomics
    - alignment
    - rna-seq
    - splice-aware
graph:
  domains: [domain:bioinformatics]
  specializations: [specialization:biomedical-informatics]
  skillAreas: [skill-area:graph-algorithms, skill-area:python-data-pipelines, skill-area:data-analysis]
  workflows: [workflow:experiment-design]
  roles: [role:research-engineer, role:biomedical-engineer]
---

# STAR RNA-seq Aligner Skill

## Purpose
Provide STAR alignment for splice-aware RNA-seq read mapping with comprehensive QC metrics.

## Capabilities
- Splice junction detection
- Two-pass alignment mode
- Chimeric read detection (fusions)
- Gene quantification (--quantMode)
- Custom genome index generation
- Output in multiple formats

## Usage Guidelines
- Generate genome indices with annotation
- Use two-pass mode for novel junction discovery
- Enable chimeric read detection for fusion analysis
- Generate quantification in addition to alignments
- Optimize parameters for read length
- Document STAR version and parameters

## Dependencies
- STAR
- HISAT2
- kallisto

## Process Integration
- RNA-seq Differential Expression Analysis (rnaseq-differential-expression)
- Single-Cell RNA-seq Analysis (scrnaseq-analysis)
- Spatial Transcriptomics Analysis (spatial-transcriptomics)


---
Source attribution: a5c-ai
Original project: https://github.com/a5c-ai/babysitter
License: MIT
License information: https://opensource.org/license/mit
Original upstream instructions; downloaded from Dave AI.

## Upstream license notice

MIT License

Copyright (c) 2026 Gabriel Moreira

Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the rights
to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
copies of the Software, and to permit persons to whom the Software is
furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all
copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
SOFTWARE.



# Dave AI resource metadata

Creator / publisher: a5c-ai
Original project: https://github.com/a5c-ai/babysitter
Attribution basis: Upstream repository explicitly recorded in package mirror path

Fields of work: Data & Analytics, Education & Research, Healthcare & Life Sciences
Roles: Clinical Research, Data Scientist, Researcher
Specialties: Specialty not specified
Tools: Star
Country applicability: Country not specified
Classification basis: Source catalog labels
Instruction SHA-256: 6a7df3c6f3ed464a5ad67ab1ca3657cfa4019f58a612ac5209378fdc92c70ad0