featurecounts-rna-counting SKILL.md skillA
featurecounts-rna-counting from jaechang-hits/sciagent-skills is an agent skill: a SKILL.md folder an AI agent loads when a task calls for it.
mdr add jaechang-hits/sciagent-skills/featurecounts-rna-counting@git:20260929.7a7d60fPins git:20260929.7a7d60f in mdr.lock. Pin the fingerprint instead.
- Audit grade
- A, 17 of 17 checks passed
- Kind
- SKILL.md skill
- Repository
- jaechang-hits/sciagent-skills
- Path
skills/genomics-bioinformatics/rnaseq/featurecounts-rna-counting/SKILL.md- Versions recorded
- 3
- Latest version
- git:20260929.7a7d60f, committed Sep 29, 2026
- First version recorded
- May 28, 2026
- Size
- 14,795 bytes
- Repository stars
- 381
- License
- a license file GitHub does not identify
Counts RNA-seq reads overlapping GTF gene features. Takes sorted STAR BAMs plus GTF; outputs a per-gene tab-delimited matrix across samples. Handles strandedness (0/1/2), paired-end, multi-sample batch counting in one command, and outputs assignment statistics. Use Salmon for alignment-free quantification; use featureCounts when STAR BAMs already exist.
Collected from public GitHub. Every version is saved exactly as it was and never changes. Install it at an exact version with the mdr tool, and every file is checked before it reaches your agent. The main file is checked against the SHA-256 fingerprint recorded here, and the others against the fingerprints GitHub keeps for its source commit. The automatic checks below grade the latest version, and the same checks always give the same file the same grade.
What the file says
# featureCounts — RNA-seq Read Counting ## Overview featureCounts (part of the Subread package) assigns sequencing reads in BAM files to genomic features defined in a GTF/GFF annotation. It counts how many reads overlap each gene (or exon, intron, or custom feature), producing a gene × sample count matrix suitable for differential expression analysis with DESeq2 or edgeR. featureCounts processes multiple BAM files in a single command, reporting read assignment statistics (assigned, unassigned by category) alongside the count matrix. It is the standard counting step after STAR alignment in RNA-seq pipelines. ## When to Use - Generating gene-level count matrices from STAR-aligned BAM files for DESeq2 or edgeR - Counting reads from multiple samples simultaneously in a single featureCounts command - Handling stranded RNA-seq libraries where sense/antisense assignment matters - Producing exon-level or custom-feature counts (e.g., for splicing analysis with DEXSeq) - Verifying strandedness of an RNA-seq library when protocol documentation is unavailable - Use **Salmon** instead when no BAM file exists and fast pseudoalignment is preferred …
Read the whole file at its exact version.
How to install
mdr add jaechang-hits/sciagent-skills/featurecounts-rna-counting@sha256:33ad4ee741a5ce15The line at the top of this page pins the label git:20260929.7a7d60f, which is what most people want. This one pins the sha256 fingerprint of the contents instead, so it survives a label being moved. Either way the exact version is written to mdr.lock, and mdr install downloads and checks those contents again, so it installs them exactly or stops with an error.
[](https://markdownregistry.com/a/art_gjmsywwuacb7xgf2)
3 badge image fetches in 30 days. What the badge shows.
Versions
The registry has recorded 3 versions of this file, between May 28, 2026 and Sep 29, 2026, about one every 62 days.
| version | committed | commit | size | audit | |
|---|---|---|---|---|---|
| git:20260929.7a7d60f latest | 2026-09-29 | 7a7d60f | 14,795 B | A | view · diff |
| git:20260929.35fe6e3 | 2026-09-29 | 35fe6e3 | 14,844 B | A | view · diff |
| git:20260528.3e3f998 | 2026-05-28 | 3e3f998 | 13,180 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 (14795 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
jaechang-hits/sciagent-skills · 381 stars · license a license file GitHub does not identify · pushed 2026-10-16 · branch main
API
GET https://markdownregistry.com/api/v1/artifacts/art_gjmsywwuacb7xgf2 GET https://markdownregistry.com/api/v1/resolve?ref=jaechang-hits/sciagent-skills/featurecounts-rna-counting GET https://markdownregistry.com/api/v1/blob/33ad4ee741a5ce1560328f20ea07c9135aa27c9c11e516cfd88e761c264bbe86
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