pipeline-rnaseq skillA
pipeline-rnaseq is agent-read markdown (skill) from ammawla/encode-toolkit: 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..
Indexed from public GitHub and served as immutable, content-addressed versions. Install it pinned to an exact SHA-256 with the mdr CLI, and every file is verified against the hash recorded here before it reaches your agent. The deterministic audit below grades the latest version, and the same file always earns the same grade.
What the file says
# 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 …
Read the whole file at its exact version.
How to install
mdr add ammawla/encode-toolkit/pipeline-rnaseq@git:20260921.4ba10c6mdr add ammawla/encode-toolkit/pipeline-rnaseq@sha256:c21c680c6b81ffa3Pin to a label to follow the author's releases, or to a sha256 to freeze the exact bytes forever. Either way the resolved hash is written to mdr.lock, and mdr install reproduces it on any machine.
[](https://markdownregistry.com/a/art_nbjd35cqgrch3x6u)
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Versions
| version | committed | commit | size | audit | |
|---|---|---|---|---|---|
| git:20260921.4ba10c6 latest | 2026-09-21 | 4ba10c6 | 28,885 B | A | view · diff |
| git:20260920.6050003 | 2026-09-20 | 6050003 | 28,879 B | A | view · diff |
| git:20260920.ce7840d | 2026-09-20 | ce7840d | 27,118 B | A | view · diff |
| git:20260321.d9029d0 | 2026-03-21 | d9029d0 | 19,939 B | A | view · diff |
| git:20260312.be32706 | 2026-03-12 | be32706 | 19,914 B | A | view |
Audit of the latest version
- pass: Frontmatter block present
- pass: Frontmatter declares a name
- pass: Frontmatter declares a description
- pass: Size between 200 bytes and 200 KB (28885 bytes)
- pass: No zero-width or bidi control characters
- pass: No instruction hidden inside an HTML comment
- pass: No link to an exfiltration or paste host
- pass: No credential-shaped string
- pass: No instruction to send local credentials anywhere
- pass: No text hidden with inline styles
- pass: No prompt-injection phrasing
- pass: No curl or wget piped into a shell
- pass: No recursive delete of root, home or parent
- pass: No instruction to read or print local credentials
- pass: No base64 blob over 200 characters
- pass: No link to a raw IP address
- pass: No script tag
Source
ammawla/encode-toolkit · 20 stars · license AGPL-3.0 · pushed 2026-09-21 · branch main
API
GET https://markdownregistry.com/api/v1/artifacts/art_nbjd35cqgrch3x6u GET https://markdownregistry.com/api/v1/resolve?ref=ammawla/encode-toolkit/pipeline-rnaseq GET https://markdownregistry.com/api/v1/blob/c21c680c6b81ffa31c9a0ca3939832f0c210b27242e3ad0aff487ed4197e7fa8
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