bedtools-genomic-intervals SKILL.md skillA
bedtools-genomic-intervals 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/bedtools-genomic-intervals@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/interval-ops/bedtools-genomic-intervals/SKILL.md- Versions recorded
- 3
- Latest version
- git:20260929.7a7d60f, committed Sep 29, 2026
- First version recorded
- May 28, 2026
- Size
- 17,306 bytes
- Repository stars
- 381
- License
- a license file GitHub does not identify
Genomic interval ops on BED/BAM/GFF/VCF. Find overlaps, merge intervals, compute coverage, extract FASTA, find nearest features. Core for ChIP-seq peak annotation, region filtering, genome arithmetic. Use tabix for indexed single-region queries; use deeptools for normalized bigWig coverage.
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
# bedtools — Genomic Interval Analysis Toolkit ## Overview bedtools is the standard toolkit for operating on genomic intervals in BED, BAM, GFF, and VCF formats. It solves the core problem of genome arithmetic: finding overlaps between feature sets, computing coverage, extracting sequences, merging adjacent regions, and annotating features with nearest neighbors. bedtools operates on sorted coordinate lists and runs at C speed, making it practical for whole-genome analyses. ## When to Use - Intersecting ChIP-seq peaks with gene annotations to find promoter-overlapping peaks - Merging overlapping ATAC-seq peaks or called regions across replicates - Computing read coverage depth over target capture regions - Extracting FASTA sequences for motif discovery or primer design - Finding the nearest gene to each regulatory element or variant - Subtracting blacklist or repeat regions from peak calls - Expanding genomic intervals by fixed distance (promoter regions) - Use `tabix` instead for fast indexed queries of a single genomic region - For normalized coverage bigWig tracks, use `deeptools bamCoverage` instead - Use `mosdepth` instead for whole-genome per-base depth (10× faster) …
Read the whole file at its exact version.
How to install
mdr add jaechang-hits/sciagent-skills/bedtools-genomic-intervals@sha256:b5563fe2fc48b66cThe 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_f323wvxlpmqf6r4o)
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 | 17,306 B | A | view · diff |
| git:20260929.35fe6e3 | 2026-09-29 | 35fe6e3 | 17,355 B | A | view · diff |
| git:20260528.3e3f998 | 2026-05-28 | 3e3f998 | 15,678 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 (17306 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_f323wvxlpmqf6r4o GET https://markdownregistry.com/api/v1/resolve?ref=jaechang-hits/sciagent-skills/bedtools-genomic-intervals GET https://markdownregistry.com/api/v1/blob/b5563fe2fc48b66c33d946801f48fec29ca5d7c72a9caeb12019514fae8d3e71
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