Individual skill

pipeline-rnaseq

Execute ENCODE RNA-seq pipeline from FASTQ to gene quantification and signal tracks. Child of pipeline-guide. Provides Nextflow execution with Docker and cloud deployment. Use when processing RNA-seq data with STAR alignment, RSEM/Kallisto quantification, or generating expression matrices. Trigger on: RNA-seq pipeline, gene expression, STAR alignment, RSEM quantification, transcript quantification, TPM, FPKM, RNA processing, run RNA-seq.

plugin/skills/pipeline-rnaseq/SKILL.md

Source commit 36836c8725fd4d20d9c851ce314f5151aea5f57c

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Yes

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Yes

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No

Observed behavior

Network or broad shell

Last checked

Nov 6, 2026

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