RNA-seq Quantification — salmon & kallisto Transcript Abundance

Quantifies bulk RNA-seq transcript abundance with salmon 2.x (the Rust rewrite; selective alignment or --sketch) and kallisto (v0.52.0, kb-python workflow), builds a decoy-aware gentrome index, runs quant with --gcBias -l A, then imports estimates via tximport/tximeta with a tx2gene map and hands differential expression to alterlab-pydeseq2. Warns that salmon 2.0 cannot read C++/pufferfish indices (rebuild every index), that --validateMappings is now accepted-but-ignored, and that 'salmon alevin' was REMOVED (single-cell now uses piscem + alevin-fry). Use when quantifying RNA-seq transcript abundance, running salmon or kallisto, building a decoy-aware index, or wiring txi…