ReddRadar
Agent skill
salmon-quantifier
Salmon pseudo-alignment skill for fast and accurate transcript quantification
Install this agent skill to your Project
npx add-skill https://github.com/a5c-ai/babysitter/tree/main/library/specializations/domains/science/bioinformatics/skills/salmon-quantifier
Metadata
Additional technical details for this skill
- tags
-
transcriptomics quantification rna-seq pseudo-alignment
- version
- 1.0
- category
- bioinformatics
SKILL.md
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)
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