pipeline-rnaseqlisted

# ENCODE RNA-seq Pipeline ## When to Use - User wants to run an RNA-seq processing pipeline from FASTQ to gene quantification - User asks about "RNA-seq pipeline", "STAR alignment", "RSEM", "gene expression quantification", or "Kallisto" - User needs to process bulk RNA-seq data with ENCODE-standard 2-pass STAR alignment - Example queries: "process my RNA-seq FASTQs", "quantify gene expression from RNA-seq", "run STAR and RSEM on my data" Execute the ENCODE RNA-seq processing pipeline from raw FASTQ files through splice-aware alignment, gene/transcript quantification, and strand-specific signal track generation. This skill provides a complete Nextflow DSL2 implementation following ENCODE uniform analysis standards. ## Overview RNA-seq measures transcriptome-wide gene expression by sequencing cDNA derived from cellular RNA. The ENCODE pipeline processes RNA-seq data through quality control, splice-aware alignment with STAR (2-pass mode), gene and transcript quantification with RSEM, optional fast pseudoalignment with Kallisto, and generation of strand-specific signal tracks as bigWig files. Key design decisions: STAR 2-pass mode for maximum splice junction sensitivity, RSEM for accurate gene/transcript/isoform quantification including multi-mapped reads, stranded library protocol (dUTP/rf-stranded) as the ENCODE standard, and paired-end sequencing with a minimum of 30 million uniquely mapped reads per replicate. ## Key Literature | Reference | Journal | Year | DOI | Re