Category:Science & Research · Sub-category: biology-medicine · Last updated:
Parses, queries, converts, and extracts from GTF and GFF3 gene-model annotation files - walking the gene/transcript/exon/CDS hierarchy with gffutils (queryable SQLite DB), converting formats and extracting transcript/CDS/protein FASTA with gffread, slurping to dataframes with gtfparse/pyranges, and sanitizing malformed files with AGAT. Covers the 1-based-inclusive vs 0-based BED coordinate conversion (start-1 only), deriving implicit features (introns/UTRs/TSS), phase-not-frame, the stop-codon-in-or-out-of-CDS convention, and the chr1-vs-1 seqid and gene-ID-version mismatches that silently produce all-zero count matrices and dropped joins. Use when extracting features or sequences from an annotation, converting GTF<->GFF3 or GTF->BED, traversing the gene tree, or diagnosing a coordinate/provenance mismatch upstream of counting or DE.
About this skill (catalog notes)
bio-genome-intervals-gtf-gff-handling includes at least one code block. At roughly 2,414 words the SKILL.md is on the longer end of the catalog distribution.
How bio-genome-intervals-gtf-gff-handling fits the catalog
bio-genome-intervals-gtf-gff-handling sits in the Science & Research category under the biology-medicine sub-topic in the ClaudSkills catalog. There are 10 related skills indexed alongside it; comparing a few before installing usually reveals which fits your workflow best.
These notes are auto-generated from features detected in the SKILL.md file and from this catalog's structure — they aren't part of the source repository.
What this skill does
bio-genome-intervals-gtf-gff-handling is a community-contributed Claude Code skill in the biology-medicine sub-category. It ships as a SKILL.md file that Claude Code auto-discovers under ~/.claude/skills/bio-genome-intervals-gtf-gff-handling--skills-gtf-gff-handling/ and loads when your prompt matches the skill's trigger.
When to invoke it: Use when extracting features or sequences from an annotation, converting GTF<->GFF3 or GTF->BED, traversing the gene tree, or diagnosing a coordinate/provenance mismatch upstream of counting or DE.
Who uses this skill
The bio-genome-intervals-gtf-gff-handling Claude Code skill is built for researchers, data scientists, academics, and analysts working with complex data and scientific literature. It's part of ClaudSkills (also referred to as Claude Skills or Claude Code Skills) — the open community-curated registry of 93,000+ SKILL.md files for Anthropic's Claude Code agent and the wider Claude ecosystem (Claude API, Claude Agent SDK).
Or just download SKILL.md directly and drop it into ~/.claude/skills/bio-genome-intervals-gtf-gff-handling--skills-gtf-gff-handling/. Claude Code auto-discovers it on next session.
Skills live at ~/.claude/skills/bio-genome-intervals-gtf-gff-handling--skills-gtf-gff-handling/SKILL.md on macOS/Linux, or %USERPROFILE%\.claude\skills\bio-genome-intervals-gtf-gff-handling--skills-gtf-gff-handling\SKILL.md on Windows. See the full install guide for step-by-step instructions.
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One-click install via the desktop app
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Pro
For the full experience including quality scoring and one-click install features for each skill — upgrade to Pro.
How do I install the bio-genome-intervals-gtf-gff-handling Claude Code skill?
Install via the ClaudSkills desktop app (one click) or copy SKILL.md from the source repository to ~/.claude/skills/bio-genome-intervals-gtf-gff-handling--skills-gtf-gff-handling/SKILL.md and restart Claude Code. Both flows are detailed at claudskills.com/install/.
What does the bio-genome-intervals-gtf-gff-handling skill do?
Parses, queries, converts, and extracts from GTF and GFF3 gene-model annotation files - walking the gene/transcript/exon/CDS hierarchy with gffutils (queryable SQLite DB), converting formats and extracting transcript/CDS/protein FASTA with gffread, slurping to dataframes with gtfparse/pyranges, and sanitizing malformed files with AGAT. Covers the 1-based-inclusive vs 0-based BED coordinate conversion (start-1 only), deriving implicit features (introns/UTRs/TSS), phase-not-frame, the stop-codon-in-or-out-of-CDS convention, and the chr1-vs-1 seqid and gene-ID-version mismatches that silently produce all-zero count matrices and dropped joins. Use when extracting features or sequences from an annotation, converting GTF<->GFF3 or GTF->BED, traversing the gene tree, or diagnosing a coordinate/provenance mismatch upstream of counting or DE.
Is this skill free to install?
Yes. ClaudSkills is an open registry — every skill keeps its source repository's license, and manual install via copy is free. ClaudSkills Pro ($9/mo, $79/yr, or $149 one-time) adds one-click install via the desktop app and a multi-signal Quality Score.
When should I use the bio-genome-intervals-gtf-gff-handling skill?
Use bio-genome-intervals-gtf-gff-handling when your Claude Code task falls under the Science & Research category — specifically in the biology medicine area. Claude Code auto-discovers installed skills and invokes the right one based on the task description, so you can also ask Claude directly (e.g. "use bio-genome-intervals-gtf-gff-handling" or describe the task and let Claude pick). Browse related skills at /category/science/.
What is a Claude Code skill and how does the bio-genome-intervals-gtf-gff-handling skill fit in?
A Claude Code skill is a SKILL.md file that lives under ~/.claude/skills/<name>/ and tells the Claude Code CLI agent how to perform a specific task (instructions, prompts, allowed tools). Skills are auto-discovered at session start. bio-genome-intervals-gtf-gff-handling is one of 67,000+ skills indexed in the open ClaudSkills catalog, classified under the Science & Research category. Learn more at /learn/what-is-a-claude-skill/.
@misc{bio-genome-intervals-gtf-gff-handling--skills-gtf-gff-handling-2026,
author = {bg-szy},
title = {bio-genome-intervals-gtf-gff-handling [Claude Code skill]},
year = {2026},
publisher = {ClaudSkills},
url = {https://claudskills.com/skills/bio-genome-intervals-gtf-gff-handling--skills-gtf-gff-handling/}
}
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