bio-clip-seq-clip-alignment SKILL.md skillA
bio-clip-seq-clip-alignment from pku-yuangroup/openai4s is an agent skill: a SKILL.md folder an AI agent loads when a task calls for it.
mdr add pku-yuangroup/openai4s/bio-clip-seq-clip-alignment@git:20260821.2d1b678Pins git:20260821.2d1b678 in mdr.lock. Pin the fingerprint instead.
- Audit grade
- A, 17 of 17 checks passed
- Kind
- SKILL.md skill
- Repository
- pku-yuangroup/openai4s
- Path
skills/bioskills/bio-clip-seq-clip-alignment/SKILL.md- Versions recorded
- 1
- Latest version
- git:20260821.2d1b678, committed Aug 21, 2026
- Size
- 20,148 bytes
- Repository stars
- 662
- License
- MIT
Align preprocessed CLIP-seq reads (eCLIP, iCLIP, iCLIP2, PAR-CLIP) to genome with STAR or bowtie2 using crosslink-preserving parameters, choosing between unique-mapper-only and multi-mapper-aware alignment for repeat-binding RBPs, deciding STAR vs HISAT2 memory trade-offs, and applying ENCODE-compatible filters. Use when turning preprocessed CLIP FASTQ into a deduplicated, MAPQ-filtered BAM ready for peak calling or crosslink-site detection.
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
## Version Compatibility Reference examples tested with: STAR 2.7.11b+, bowtie2 2.5.3+, HISAT2 2.2.1+, samtools 1.19+, CLAM 1.2+, umi_tools 1.1.5+. Before using code patterns, verify installed versions match. If versions differ: - CLI: `<tool> --version` then `<tool> --help` to confirm flags If code throws unexpected errors, introspect the installed binary (`<tool> -h`) and adapt the example to match the actual CLI rather than retrying. # CLIP-seq Alignment **"Align preprocessed CLIP reads to genome with crosslink-preserving parameters"** -> Map UMI-extracted, adapter-trimmed reads to the genome (NOT transcriptome) with end-to-end alignment, strict mismatch ceiling, and unique-mapper-only filtering by default. The 5' end of the read (R2 5' in paired-end eCLIP; R1 5' in iCLIP) carries the reverse-transcriptase truncation = crosslink site -1; any soft-clipping or 5' trimming during alignment destroys nucleotide resolution. …
Read the whole file at its exact version.
How to install
mdr add pku-yuangroup/openai4s/bio-clip-seq-clip-alignment@sha256:6a407f204a43f73dThe line at the top of this page pins the label git:20260821.2d1b678, 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_qgrejqgcx6qkk4vg)
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Versions
The registry has recorded 1 version of this file, committed on Aug 21, 2026.
Audit of the latest version
- pass: Frontmatter block present
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- pass: Frontmatter declares a description
- pass: Size between 200 bytes and 200 KB (20148 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
pku-yuangroup/openai4s · 662 stars · license MIT · pushed 2026-11-03 · branch main
API
GET https://markdownregistry.com/api/v1/artifacts/art_qgrejqgcx6qkk4vg GET https://markdownregistry.com/api/v1/resolve?ref=pku-yuangroup/openai4s/bio-clip-seq-clip-alignment GET https://markdownregistry.com/api/v1/blob/6a407f204a43f73d888447b6b74bd53c81aa029b2c73db481ba172e8d5131b1f
Your AI assistant does the legwork. You hear about the deals worth your word. Hand yours the standing instructions at modelranch.com and it joins the network that reads files like this one.
Guides: the SKILL.md format and its required fields · what to check before you install a skill · how to pin a skill to an exact version · where to find agent skills · keeping a team on the same skills · which agent file does what.