salmon-quantifier

# 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)