Salmon Quantifier
Documentssalmon-quantifierSalmon Quantifier is an Agent Skill for documents published in the a5c-ai/babysitter repository on GitHub: a SKILL.md instruction file an AI agent can load to do this task.
Salmon pseudo-alignment skill for fast and accurate transcript quantification
QUICK START
How to use this skill
Bring this guide into your coding agent with a prompt tailored to the tool you use.
- Open your project in Codex.
- Copy and paste the prompt below.
- Review files and risks before approving any action.
Prompt to paste
Inspect the Agent Skill at https://github.com/a5c-ai/babysitter/blob/HEAD/library/specializations/domains/science/bioinformatics/skills/salmon-quantifier/SKILL.md and all supporting files. Report provenance, permissions, scripts, dependencies, and security risks. Propose an exact installation into .agents/skills/salmon-quantifier, but wait for my approval before writing files or running scripts.
Copying this prompt does not install or run the skill. Review third-party files before use.
Salmon Quantifier Skill
Purpose
Enable Salmon pseudo-alignment for fast and accurate transcript quantification.
Capabilities
- Selective alignment mode
- GC bias correction
- Mapping rate assessment
- Bootstrap uncertainty estimation
- Multi-mapping resolution
- Decoy-aware indexing
Usage Guidelines
- Build decoy-aware indices for accuracy
- Enable GC bias correction
- Use selective alignment for improved accuracy
- Generate bootstraps for uncertainty estimation
- Validate mapping rates against expectations
- Document index and parameter versions
Dependencies
- Salmon
- kallisto
- RSEM
Process Integration
- RNA-seq Differential Expression Analysis (rnaseq-differential-expression)
- Single-Cell RNA-seq Analysis (scrnaseq-analysis)