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)