RNA-seq Quantification — salmon & kallisto Transcript Abundance

The command-line quantification entry point for bulk RNA-seq: take raw FASTQ reads plus a reference transcriptome and produce transcript-level abundance estimates (counts + TPM) with salmon (selective alignment) or kallisto (pseudoalignment via kb-python), then aggregate to the gene level with tximport/tximeta and hand off to alterlab-pydeseq2 for differential expression. It is the raw-data-to-count-matrix pipeline that the repo's Python analysis skills assume already ran.

Quick Start

Quantify these RNA-seq FASTQs with salmon and a decoy-aware index
Build a salmon gentrome index from this transcriptome + genome
Run kallisto / kb count on my paired-end reads
Turn my salmon quant.sf files into a gene-level count matrix for DESeq2