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)